Dragon Ball was originally a comedic version of Journey to the West. The villains were largely silly, like Emperor Pilaf and Commander Red, but then Krillin got killed by a monster (he got better). The monster was Demon King Piccolo, who wanted eternal life, and after this arc and the Piccolo Jr. arc, the comedic elements slowly decreased. This quickly became evident when Raditz, Goku's older brother, came and told Goku that he was an alien from another planet who was supposed to kill everyone on Earth. Toei, the company in charge of the Dragon Ball anime, decided then and there to end Dragon Ball and rename it Dragonball Z, starting with the arrival of Raditz.
The Buu saga drifted somewhere to the middle and the more recent 2008 Jump Tour special had a heavy emphasis on comedy over action, which many fans seemed to find rather refreshing.
Toriyama was aware of this effect to some degree. He introduced the Ginyu Force just to relieve some of the tension from the escalating villains (Raditz -> Nappa/Vegeta -> Zarbon/Dodoria -> Frieza). Of course, just because the Ginyu Force are silly to the point of being buffoonish doesn't mean they aren't extremely dangerous.
One Piece villains have gotten more serious as the series went on. At first, the villains could be easily defeated with only minor injuries to the heroes (like Buggy). Later on, they could actually defeat the heroes, only to lose in the rematch (like Crocodile). Now, there are SO many villains that can or have easily defeated Luffy in battle (Kuma, Kizaru, Magellan, Aokiji, Mihawk, must I continue?).
And don't forget the fact that the series, while still light and soft for the most part, has started to focus on themes such as slavery, racism, political corruption, anarchy, segregation, and moral absolutism. And the most recent story arc has drawn historical parallels to violent black supremacy groups, the KKK, xenophobic practices of ancient Japan, and Al Qaeda (all at once, mind you).
Kinnikuman started off as a comedy series parodying Ultraman, but then became a wrestling series with loads of drama, although with very silly characters.
The anime adaptation of Trigun has a variation; all the filler is in the beginning, so it begins as a silly series with occasional bouts of action as the "insurance ladies" track down the identity of Vash the Stampede, then slowly come to accept that the goofball they found is a legendary gunman and walking disaster. About halfway through the series, actual plot from the manga starts appearing in consecutive episodes, with Knives sending the Gung-ho Guns, a team of ruthless super-powered fighters after him. Ostensibly they're hired to kill him, but really they're meant to make Vash suffer, which they all succeed in, each in their own way. This changeover is also evident in whether or not Vash manages to successfully keep people from getting killed; he manages it easily for the first half the series, but in the episode where the change hits you get streets littered with the corpses of men, women, and children.
It gets worse in the manga. To illustrate: there is an entire demographic change (Shonen-- school-age kids-- to Seinen-- adults).
CLAMP's Tsubasa Reservoir Chronicle started out as a fairly upbeat and child-friendly adventure story, but took a sudden turn for the Angst in the Acid Tokyo arc, almost exactly the halfway point of the series. The arc's post-apocalyptic setting -- where Tokyo is a desert and the only rain is acid -- pales in comparison to the revelations of treachery and hints of almost unimaginably horrific Backstory. There is simultaneously a dramatic increase in the prominence of death, violence, and sexual tension. The tone does become more hopeful again in the last third of the story, but the seriousness remains throughout. Tsubasa seems be a case of deliberate Cerebus, to the point of the second half essentially deconstructing the first and showing that its happiness and innocence was enabled by darkness lurking behind the scenes.
Only adding to the angst is that Syaoran's decision to turn back time so he could save Sakura's life caused the entire multiverse to start decaying. Space-time was altered so much that Acid Tokyo and Clow Country are actually in the same world; the mysterious ruins that Syaoran enjoyed investigating so much were the ruins of Acid Tokyo, after all. But the heroes never did have the ability to time travel. Oh my.
Da Capo literally tells the viewer in a next episode preview halfway through the series that it's about to get serious. And it does.
Mahou Sensei Negima began as a light comedy about an inept ten-year old mage teaching a class of 31 Japanese middle school girls with lots of Fan Service. As the arcs progressed, the story became much more action-oriented and fairly serious at times.
Witch Hunter Robin started with the "monster of the week" style then shifted gears into plot and drama halfway through.
Bleach, while still incorporating darker elements, started out as something of a Slice of Life story with a Fish Out of Water situation and a bit of a Monster of the Week feel, with more focus on characters and their stories rather than action, but then they finished defining the starting characters and the Soul Society arc kicked the series into high gear. They STILL try to squeeze in elements from the first season whenever possible... apparently, to remind the viewer what they are watching!
GetBackers starts out as a fairly standard We Help the Helpless series about two teenage guys having dorky misadventures, but the introduction of the other four major characters brings along the revelation that they have incredibly angsty back stories, involving Ginji becoming a crazy sociopath if he's not careful and Ban killing at least two of his friends, and lots of Parental Abandonment. Happily, the pair retain their status as a Weirdness Magnet and are still capable of being incredibly silly at the drop of a hat, so the slide isn't too drastic.
Fruits Basket started as a manga with a balance between humor and drama with some physical comedy and some sadder stories about the character's lives. Near the end, story arcs about the true nature of the curse, and Kyo's eventual being locked away predominated.
Toradora! starts out mostly comedy with a little drama on the side, gradually sliding the slider from comedy to drama as the arcs go on.
GaoGaiGar to GaoGaiGar Final: The light-hearted original series did dip its toe into seriousness every so often, but it was primarily a fun super-robot show. With the release of the OVA Final it goes into darker and edgier territory. By the second episode...One character's lover is killed by what appears to be the cute kid lead of the series, who is himself killed by the main character. Then, said main character is captured by the villains and brainwashed into fighting the good guys. And in the final episode, despite having defeated the Big Bad, all but two members of the main cast are trapped at the other end of the galaxy, dying, and with no foreseeable way to get back to Earth. Nevertheless, the OVA remained true to the series' central theme of courage overcoming opposition throughout - it merely explored some of the more dramatic aspects of fighting a seemingly hopeless battle against a seemingly invincible foe.
Detective Conan started as a mystery-themed comedy just like how Gosho Aoyama did with kendo in Yaiba. With time it has developed into a more serious story--which made the animators who guessed too much making a few Schrodingers Cats.
Mobile Suit Gundam ZZ initially starts out with the old monster of the week routine with plenty of campy slapstick comedy despite the fact that it's not anime. Then episode 18 rolls around and the story starts picking up momentum, and the comic mischief is eventually displaced by more serious content. By the time it becomes anime, the tone of the series becomes something more along the same vein as Zeta Gundam.
The first half of Neon Genesis Evangelion, while still dramatic, is actually somewhat light-hearted at times. Then the series slowly shifts to being disturbing and insane. Though it was always rather introspective to begin with, it doesn't quite compare to later half. Then ItGotWorse.
Second half: boy's giant robot turns out to contain the soul of his mother, boy undergoes psychological and existential breakdown, boy ends the world by ending human individuality, and boy tries to strangle his friend when they are the last two humans seen alive in a post-apocalyptic wasteland.
You could argue that the first half of the show is a bit of an inverse Cerebus; the first few episodes are quite dark and moody, certainly not comedy material, although there are a few funny moments. It's not until after the Fifth Angel fight that Shinji begins to open up a little, and the tone of the show lightens correspondingly - basically peaking at the infamous "thermal expansion" jokes. And then you hit the second half of the recap episode and things start going south again.
Self-published manga Onani Master Kurosawa (given the Fan Nickname "Fap Note") starts out like a goofy parody of works like Death Note, with the main character having over-the-top monologues and carrying out masturbation-related revenge against some classmates. However, it doesn't take long before it turns more angsty and dramatic with love triangles and themes about coming of age (pun not intended).
For the first season at least, the series seems to contract Cerebus Syndrome exactly once an arc, beginning as a typical Unwanted Harem before regularly bringing out the terrors, with progressively less time in between the two, until approximately the second arc of Kai.
Yu-Gi-Oh! GX. Third season, just about one third through. Suddenly there are people actually dying. And then they go back to the alternate world thing and it just gets worse. See also: Yubel. It's worth noting that said dead people do come back.
Well, Judai's friends come back. No word on Amon, Ekou, or all the people Judai killed for Super Fusion.
It is good to note that this is hilariously parodied in DarkSideIncorporated's Yu-gi-oh Gx abridged series.
The second season continues this as it gradually becomes Darker and Edgier as the series goes on. Though this should be noted as only happening in the manga, in the anime the second season continues to be a Romance Comedy.
The infamous School Days starts off as a rather typical bishoujo comedy with a love triangle, but soon plummets into drama, violence, and downright insanity. It has long been notorious for such same elements in its original video game and for its brutal ending paths of which the anime adaptation decided to stay true to. Many unlucky saps fell for the anime who weren't aware of this fact.
While it never permanently slipped into this, Keroro Gunsou got some more serious moments as the series progressed. You're watching (or reading) this hilariously cute story with these frogs who never get any invading done. You expect Status Quo Is God to remain in affect forever and nothing bad to ever really happen to the planet, then suddenly the entire planet is put into paralysis by a much more dangerous platoon who has come not only to take over the planet but also to discharge the Keroro Platoon. To add to it, Keroro is in the middle of being de-aged and losing his memory, Giroro gets shot out of the sky by his brother and we don't know if he's alive for a while, and we learn that when a platoon is discharged, the members of it are supposed to separate forever. OUCH.
Yu Yu Hakusho started out as a wacky comedy about a tough high schooler who dies but gains a chance at returning to life by doing good deeds as a ghost, mining comedy from the fact that Yusuke can't really figure out how to do a "good deed" without being violent, rude, or abrasive. This led to a mostly episodic series of adventures as Yusuke and his guide Botan wandered the city finding people in need of help and playing Clarence to their George Baily. Then after about 30 chapters of this, Yusuke gets brought back to life, discovers he has superpowers now, and is given a job as a "spirit detective," which basically involves beating up bad guys connected to the afterlife. YYH becomes an action fighting series and the comedic formula is dropped permanently.
In a way, Yu Yu Hakusho actually went through Cerebus Syndrometwice. After becoming Spirit Detective, Yusuke had to do some semblance of actual detective work, tracking down fugitives and recovering magical items they'd stolen rather than just beating them up (though he did that too). Botan was set up as his assistant, proving him with detective tools and passing on his assignments from Koenma. This lasted for exactly one story arc, after which the series shifted into a simpler shonen fighting formula. With a two great big Tournament Arc.
After the Chapter Black Arc, in which it is revealed (as hinted at by Hiei and Kurama becoming good guys) that not everything is as cut-and-dried as the previous theme of "Yusuke and Friends vs. Demons" action stories led us believe, the story suddenly becomes extremely character-driven, exploring Yusuke's disconnection with his formerly "normal" existence, Kuwabara's resolve to become something productive, Hiei's finding a new purpose in life, and Kurama resolving his demonic past. This is especially notable in the anime, where the first third of the Three Kings Arc has nearly NO fights, instead being low-key character pieces about Yusuke, Hiei, and Kurama, effectively going through Cerebus Syndrome twice as it evolves from an offbeat comedy to action show, then suddenly to a more character-driven series rather then the less serious and more action-oriented shonen Fighting Series.
This does not happen in Ranma 1/2, unless one counts the Ryu Kumon story arc- if anything, the series actually has a reversed form of this, starting out fairly serious (if comedic) and transforming into more or less slapstick plus dramatic moments. The fandom, however, is known for its creation of drama and angst Fan Fiction, evidently based on the fact that a lot of the series' humor does stem from Comedic Sociopathy, "you gotta laugh or else you'll cry" moments, and bits that ring uneasily if you think about it enough. For example, at one point in the manga, Akane demands Ranma throw a fight in the belief that this will reduce his Unwanted Harem. When Ranma refuses, she casually uses a cat to terrify him into obedience, despite knowing how badly they scare him and all about the childhood trauma that made him so afraid of them. Ryoga having No Sense of Direction is quite easy to play for angst, given that Ryoga himself does this in canon.
In addition, during the manga, Kuno is implied to make two attempts at raping an unconscious Ranma.
Nabiki sells Ranma as a slave to some yakuza to cover a restaurant debt and is surprised he escaped.
Gosunkugi makes repeated attempts to mind control Akane or Ranma in a world where magic works.
Shampoo has tried to drug Ranma into compliance.
Kodachi out right states she knows Ranma doesn't love her, but pretends that he does.
Making Kodachi top on the list of most likely Ranma characters to commit suicide.
The best way to describe the Cerebus Syndrome of Hayate the Combat Butler in the last fifty chapters or so (200-250~ when you discount the missing chapters) is that it's started taking itself seriously. Not that it loses the humor entirely, but still. Hello Athena, and hello drama.
Of course, once the Athena situation is dealt with, the next mini-arc involves the cast trying to move into an apartment building that's haunted by ghost cats, who possess Izumi and turn her into a catgirl. My neck hurts for some reason...
Gakuen Alice started as an upbeat, sparkly shojo tale about a girl discovering she has superpowers (basically) and going to a school with lots of other kids with superpowers. Predictably, wacky hijinks and love triangles ensue. To be fair, there have always been hints of dark things going on in the background, but the focus was on the humor and warm fuzzies. Then around chapter 90 the series took a nosedive into severe angst.
Excel Saga parodies the bejesus out of this in its penultimate episode, in which Excel finally notices that Il Palazzo keeps killing her. Of course this is just serves to throw the last episode ( "Going Way Too Far") into sharper relief.
Ouran High School Host Club begins as an Affectionate Parody of shoujo manga, and while it doesn't leave its comedy behind, its storyline has gotten gradually more dramatic as it has gone on - particularly once it lapses out of Comic Book Time and two of the main characters actually graduate from high school and start attending university. (Early volumes, in contrast, state in the narration that no one will be moving up in grades and the seasonal changes are purely aesthetic.)
This starts to happen at the end of Konjiki no Gash!!, mostly in part due to the seriousness of the King Festival (the winner has the power to kill any and all demons he wishes, and Clear Note wants to kill every single one. Not to mention that he has shown clear intention of wanting to destroy the Earth as well.) Near the start of the arc, though, the author gets out his last hurrah of comedy in one of the most bizarre manga chapters ever written: a dream sequence which involves Sunbeam dressed up as a butterfly, him giving Kiyomaro wings and making them both fly into the sky by madly flapping their arms about, Brago wearing a lion's head for underwear (and nothing else), Sherry tossing tennis balls at Brago (who proceeds to laugh as he swats them around), the teacher's wife's head becoming that of a dog, Victoreem carrying Kid around in a cart (after which Kid pummels Victoreem), both of them slipping on banana peels, Dartagnan dressing up as Professor Riddle and tricking Kid, Dartagnan knocking Kid out with a tranquilizer dart, Dartagnan falling into a pile of crap (only for Reira to give him a rope to grab onto and swing out, only to fall into another pile of crap), Gash, Umagon, Tio, and Kiyomaro dancing dressed up as otters, and not to mention everyone wanting to slap him silly. Needless to say, it is never mentioned ever again.
Mai-HiME follows the 'intentional' version of this trope. The first half of the series is generally light and silly, corresponding to the usual Magical Girl series. But as a few early scenes hinted at, It Gets Worse in the second half. The same can be said for Mai-Otome.
Later volumes of the romantic comedy Ai Kora are less comedic and more dramatic. The twelfth volume is probably the peak of this.
Gunbuster and its sequel Diebuster were masters of this. They both had a fairly cheerful if a bit dramatic character drama going up until the magic episode, when everything started going to hell.
Soul Eater picks up this trope and takes it home. It started off as a comedic couple of one-shots about a few kids who were Death's apprentices, screwing up while trying to graduate. Cue 70 chapters later and we have (*cough cough* ahem): Mind Rape; actual rape; horrors Up to Eleven (including taking someone, draining them of their blood and then wrapping them up in their own skin to rot for eternity); arguing and trying to resist against the nature of insanity with each of the characters getting closer and closer to their breaking point; deals with the voices in your head; and blood that will tear your mind out. Literally! It started to get Darker and Edgier at the point where Ashura got introduced and it... just kept getting darker. And darker. Aaaand darker...
As the series manages to maintain its warped sense of humour and fanservice in many of its darker moments, the Knight of Cerebus in this is undoubtedly Medusa. Asura brings the Nightmare Fuel, but he is largely inactive. The meddling of Arachne and Noah pale in comparison to the Complete Monster that is the Gorgon lady.
Genshiken starts out as an introspective manga on otaku parody and college life but somewhere along the way it transforms into romance... more romance... and occasional forays into yaoi parody. Cue magazines being ripped to shreds and posted on the internet.
Even Kanamemo wasn't immune to this, but not as serious as some examples, as the show goes from complete comedy with minor drama moments to more of a dramedy (the 13th episode does bring back the comedy full force, though).
The Breaker started out as a fairly lighthearted action Manhwa with plenty of comedy thrown in, but gradually got more serious as a major character's Dark and Troubled Past (and its present consequences) comes to light. By Volume 10 the humor is entirely gone and another major character has been killed off.
Future GPX Cyber Formula was originally a typical shonen adventurous/hopeful sport anime with a few good drama parts in it. The show however, gets more dramatic and less comedic as the OVAs were released. The Double-One arc deals with Knight Schumacher/Osamu Sugo's dramatic problems (namely, his eye problems stemming from an incident with Smith in the TV series which nearly rendered him blind), ZERO builds the angst out of Asuka Sugo and Bleed Kaga, SAGA has more dramatic villains (Nagumo in particular) and SIN caps off the series with very little comedy left to it and Kaga's full-blown angst because of his jealousy towards his ex-pupil, Hayato.
However, this is somewhat justified since the director probably intended to do the shift. Also, the director's wife became the head writer for SAGA and SIN and he has consulted her since the TV series.
Now and Then Here and There arguably does this, though it happens very early on. From the majority of the first episode, one could be forgiven for thinking it was some kind of lighthearted adventure in a fantasy future. One would also most definitely be scarred for life from the shock of how wrong that assumption turns out to be.
The Fullmetal Alchemist manga somehow managed to be lighthearted and funny for its first few volumes, despite Edward and Alphonse's relatively dark backstory. The story suddenly caught Cerberus Syndrome when Hughes was killed.
The 2003 anime adaptation intentionally follows this general trajectory; despite the brothers' tragic backstory, the early episodes are generally lighthearted, with only occasional hints of darkness around the periphery. About a quarter of the way through, the show begins to get progressively darker, leading up to a halfway point where Hughes is murdered, much like his manga counterpart above. Oddly enough, from there it somewhat resets itself; the following episodes go back to being somewhat lighthearted, then get gradually darker until, by the end of the series, the story has evolved into outright tragedy.
The Golden Boy manga. It starts in a somewhat formulaic way following the happy-go-lucky wanderer Oe Kintaro and his misadventures with attractive women. Then at some point a weird techno-sex cult run by a former childhood friend comes up, Kintaro gets relegated to a side character and the manga gets increasingly wordy with confusing and lengthy arguments about the ills of society, mind control, etc. None of this appears in the anime version, which is far better known.
Digimon Adventure. While at first it seems like a light hearted comedy/adventure, it becomes increasingly serious after the introduction of Myotismon.
This is actually a pretty standard formula for Digimon series:
Digimon Adventure 02 doesn't start off as light-hearted as the first one...but the first third or so of the series is quite light-hearted with the digidestined enjoying adventures while thwarting the Digimon Emperor and his slaves. Then it becomes a lot more serious once he's defeated and The Man Behind the Man is revealed.
Digimon Tamers starts off as a Slice of Life series. Then all of a sudden, some stronger opponents appear to challenge the tamers...then a weird kid, a government agency tries to wipe the digimon out, and that's before they actually go to the digital world!
Digimon Frontier starts off rather light-hearted, but then starts to become a lot more serious with the occasional "Fun break" once Grumblemon appears. Heck; the first Big Bad Cheribumon is mentioned briefly during the first couple episodes.
Digimon Savers also follows this formula; becoming a bit of a comedy/adventure following DATS acting as a benevolent form of "Digimon police". Then Mercurimon shows up...and the trope really begins to kick in. And it gets even darker when Kurata shows up.
Love is in the Bag suddenly shifts its tone significantly by the end of Volume Three, with the revelation of the nature of Kate's "condition".
Nerima Daikon Brothers is a cheerful episodic anime musical about three struggling musicians and their pet panda trying to raise money to build a dome to perform in. Then the last four episodes turn into an extended political satire of and attack on the then Japanese Prime Minister's efforts to privatize the Japanese Post Office, complete with a much more dramatic tone, characters turning on each other, and an army of pandas getting brutally beaten up by the Prime Minister's personal guard. It will also make very little sense at all if you don't read the liner notes.
The World God Only Knows begins as a comedic manga about a Dating Sim otaku being forced to live through what amounts to a real-world Dating Sim (admittedly, it's on pain of death) in order to exorcise "Runaway Spirits". After the Goddess Diana appears, things start to get darker, with it being revealed that the "Runaway Spirits" are in fact the escaped Demons of Old Hell (called "Weiss") and that Diana and her sisters are necessary to seal them away again. This culminates with perky idol Kanon (who happens to be the host of a Goddess) being stabbed by a member of a terrorist group seeking to revive Old Hell (equivalent to the normal idea of Hell, whereas New Hell is more of a neutral "Underworld"). It still has comedy, but things are certainly getting darker...
The first 12 episodes of Revolutionary Girl Utena are pretty lighthearted, despite being weird. It´s from episode 13 where things start to turn darker. And weirder.
Fushigi Yuugi started out as a fairly typical shojo romance where a girl gets sucked into another dimension that has a mix of comedic and dramatic parts. But then the second half of the series took a darker turn when Tamahome comes home to find his family brutally murdered, and things got even more worse when more characters started to die.
The Kyou Kara Maou anime has self-definition, personal responsibility, and war being bad as themes from the start, but it's generally a very lighthearted and wacky show, with Yuuri showing a certain amount of Medium Awareness, Gunter and Wolfram's lovesick antics being Played for Laughs when they're honestly pretty creepy, slapstick moments, and many humorous resolutions to dramatic situations. Then Yuuri gets summoned by someone other than Ulrike, and the last thing he sees as Conrad sends him home is his godfather's left arm arcing through the air as the church burns and the faceless knights close in...
Because he doesn't know quite what went down, he stays relatively lighthearted himself until Conrad reappears as an enemy. He is capable of being distracted and has hilarious hijinks like his sled race with T-chan, and even his angst Heroic BSOD when he sees the Shimaron Knights again involes a tidal wave of tea.
Wolfram, on the other hand, enters a hugely intensified phase of his Character Development arc beginning with his Skyward Scream at the burned church, and everybody makes some character progress, even Yozak who didn't really need it. The 'Conrad Arc' does its Cerberus thing. And then the nuclear-bomb allegory plotline begins.
The show never actually stops being funny -- Mama-chan helps puncture the moment, when nothing else can, although the two notable instances of this in the finale build-up are Crazy Awesome and Crowning Moment of Heartwarming respectively. Still, the level of drama and darkness gets a serious kick somewhere in this arc ( which is also when Murata becomes an active character, contributing both deep depressing info and gags) and never dies down to the previous level again.
While all media of this series start in the same place, with the hero being flushed down a toilet into a fantasy world where he's king, the novels get much Darker and Edgier than the anime ever does, ditto the manga, which is adapted independently from the original novels and makes everyone longer and prettier. A few books back, for example, Yuuri mistakenly attacked Wolfram in a dark room and nearly killed him.
The manga also makes Wolfram, a lead role in his own right, a more prominent character from the start--instead of just Conrad's necklace after the first visit, for example, Yuuri's also got a brooch Wolfram chose for him, but that was removed partly because it lessened the impact of the necklace, which actually mattered, and because they'd planned out a Character Arc that involved Conrad steadily falling back as his most important Shin Makoku relationship as Yuuri bonds more closely with the others, allowing Wolfram to come into his own in a more meaningful way.
Puella Magi Madoka Magica started off like a fairly regular magical girl anime that promised sugar, hugs and happiness all around until Mami gets her head bitten off suddenly and very gruesomely at the end of EP 3, gut punching any unaware viewer like so many tons of bricks. The rest of the show only gets worse too.
To be fair, the very first scene was a pretty intense, the Deranged Animation by Studio Shaft prevented things from getting too lighthearted, and there was a fair amount of Foreshadowing as to what kind of show this would become. "Sugar, hugs and happiness" is pretty far off the mark. It doesn't help though that the happy-go-lucky opening titles stayed the same even as the show got more injections of nightmare fuel, effectively creating a pretty jarring smash-cut from titles to show in the last few episodes.
The opening titles? You mean, the opening titles where poor Madoka was stumbling, crying, running through the city to some unknown goal, or alternately depressed and in bed? It was obvious far before episode three what was going on, even without knowing whose show this was.
Naruto receives a shot of Cerebus Syndrome every now and then. At first this show was about the lovable Naruto and his comedic antics with a dark backstory lightly touched upon. Then Team 7 went on their first C-ranked mission a few episodes in and suddenly the stakes are raised to potential death. Then Orochimaru decides to invade the Leaf Village near the end of the Chunin Exams which only had one plotline death (the Third Hokage) but more lives were at stake then before. After the timeskip, Akatsuki takes the role of main antagonists (Orochimaru is put on the side) and they have plans of world domination. They even go so far as to kill Asuma, Shikamaru's sensei, which greatly affects him. The latest dose happens in the Pain arc, where Pain invades the Leaf just like Orochimaru, but actually causes several plotline deaths and devastates the Leaf village even more. Though the characters killed get an Author's Saving Throw via Nagato's sacrifice.
Tiger and Bunny started out as an Affectionate Parody of the Superhero genre with rather comedic and harmless villains. Then we're introduced to Lunatic -- a Knight Templar who is the first opponent to be treated completely seriously and to kill somebody (though the humour was back when he wasn't around). His appearance was followed by the introduction of Jake Martinez, who defeats a number of heroes one after another while holding the entire city hostage in what can be considered the first truly Wham Arc of the series. Since ep.15, every episode has a serious tone and a good dose of drama; Lunatic's tragic backstory is downright depressing. The comedy never disappears completely, but it takes a back seat to more serious plot points.
To be fair, even early episodes had their share of vague foreshadowing, so more Genre Savvy people could've seen what was coming. It might even be intentional, considering how much tribute the series pays to Western Superhero comics - all of which suffer pretty badly from Cerebus Syndrome themselves.
Believe it or not, Ah! My Goddess is not immune. Its Nifhelm Arc has the group literally going through hell for the purpose of stopping the radicals who usurped Hild to prevent a destructive war between heaven and hell. This is a manga normally best summed up as Slice of Life and Magical Girlfriend, by the way.
Ghost Sweeper Mikami gets into the syndrome once Ashtaroth starts getting prominent (although you could arguably trace it back to Medusa's introduction). However, Shiina never lets this obstruct the original comedic qualities, leading to a pretty fair amount of Mood Whiplash.
Haibane Renmei is initially quite cheery and light-hearted, but roughly half-way through shifts into something darker and much more dramatic.
Mawaru Penguindrum starts as a wacky series about the Takakura brothers's tragicomic attempts to keep their sister alive. By episode 8, we learn that the people involved in this are quite more complex and flawed than they look, but there's still quite a Mood Whiplash. By episode 18, not only more secrets and complexities are revealed (alongside many Freudian Excuses), but one character straight up tries to kill another and almost manages to kill said chara and maim another. And by episode 21, after MANY other reveals, shit has hit the fan like whoa. It Got Worse, indeed.
Gosick has a case of this, with the tension and scale of the story underlying each mystery building greater and greater towards the climax, eventually dropping the romantic comedy scenes altogether.
Slayers loves this trope, at least in the anime, to the point that you can almost track where you are in the season by it- in the first quarter it's a hilarious episodic comedy about the party's adventures on the road fighting bandit troupes, various amusing monsters, and other random events, with hints of fore-shadowing and plot dropped in, usually for more laughs. At the half-way point, things go darker, with the introduction of the first major enemy, who's usually somewhere on the way to destroying the world. At three-quarters, it's back to comedy, though slightly darker and with a bit more plot than the first quarter. In the last quarter, it's back to the dark stuff, and time to take care of the Big Bad for good.
The Wandering Son manga started out pretty typical - it had lighthearted moments and mature moments but it wasn't so bad. Once puberty started kicking in more viciously and the characters entered middle school it slowly became less comedic and more angsty. It's a Justified example though, and probably intentional.
Narutaru starts off like a reasonably series before quickly becoming a Mind Screw full of horrors. It's a very intentional example.
As was the author's next series, Bokurano. It starts off looking like a retreat to '70s and '80s style Super Robot Genre about middle-schoolers saving the world with a giant robot (in terms of overall story - more Genre Savvy viewers quickly noticed the odd lack of comedic antics from the main characters and strangely apathetic and cynical behavior of the scientist that chose them to pilot the robot.) things quickly get worse. In fact, the author is famous for using this trope to deconstruct typical kids' genres of anime. When he announced that his latest work would be about a boy who rides his bike ad loves fishing, many people started to produceridiculous theories about how the boy's bike would destroy the world.
Popotan is in no way only comedic to begin with, but even so its first couple of episodes at least has more laughs than tears. The later ones do not. The biggest example is without a doubt Konami's death in episode 9, which marks the transition from dramedy to regular drama.
Happens once in a while in Gintama. The Benizakura, Itou, Yoshiwara, Jiraia, Kabukichou (and other) storylines are way more serious and dramatic than the usual lazy-ass, nose-picking, potty humored regular episodes. Also, any time Takasugi shows up, shit gets serious. And then he goes away, and the series goes back to the normal idiocy. It's also notable that even in the serious stories, the series still maintains a certain level of dorkiness.