Square Enix probably loves this trope even more then Disney does. It's almost a rule that Square-Enix games MUST have a giant transforming final boss(if that was not already evident from the fact that it has its own dedicated huge category).
Sephiroth from Final Fantasy VII, whose Ominous Latin ChantingLeitmotif is the Trope Namer (having one wing). He began as a human, then transformed into the aptly named Bizarro Sephiroth, a coccoon for what he intended to be his ultimate form, the angelic Safer Sephiroth. In the same game Hojo goes through two stages of mutations before dying.
Final Fantasy IV had Zemus the Lunarian wizard transform into the demonic insectoid Zeromus, which transforms into a more boney form when the heroes shine the light of the Mineral MacGuffin on him. Various bosses also do this - Scarmiglione transforms into an undead monster, Baigan turns his arm to snakes, the Dark Elf transforms into a dragon, and several monsters show up on the map as hooded, cloaked figures, although if that is actual transformation or just a limitation of map sprites is unclear.
FFV had Exdeath twice, first into his true form of a sentient evil tree, and then into a hodgepodge of various monsters out of the Void when he learns that Evil Is Not a Toy and becomes Neo Exdeath.
Also Gilgamesh, who gets extra arms and more demonic looks.
FFVI had Kefka, who in the final battle reveals he's become a Physical God and is now a grotesque Fallen Angel with light purple angel wings and black demonic wings.
Final Fantasy VIII had the fake president turn into the zombie Gerogero. And Ultimecia, who just gets progressively weird looking as the battle continues.
Final Fantasy XI is a bit more reserved. The Shadowlord and Promathia (initial release and second expansion) have two-stage battles, but rather than undergoing a physical change for the second stage, they just get a new set of abilities and a fresh HP Bar.
The third expansion features three bosses back to back in the final battle, though the final one, Alexander, takes over the fight himself after you deal enough damage to the Prince who is piloting his current body. This is played a bit more straight in the first expansion, Rise of the Zilart when Eald'narche is knocked off his floating platform and his eyepatch comes off, revealing a glowing eye and he starts flying for the rest of the fight. Lady Lilith plays this traditionally straight, going from her normal attire to Lilith Ascendant for Round 2.
Final Fantasy XII had Vayne turn into a gigantic clockwork dragon with the help of his rebel Occuria pal. And before that he used the power of nethicite to Hulk Out and become Vayne Novus.
Final Fantasy XIII features Galenth Dysley, who masqueraded as a frail old man and the leader of the Sanctum. His true form is the giant-robotic-rape-face fal'Cie Barthandalus.
Orphan, the true final boss, has his own one-winged angel form. Which makes it a one-winged angel form of a one-winged angel form.
And in Final Fantasy XIII-2, Caius has two One Winged Angel forms; the first being a Palette Swap of Fang's Eidolon, Bahamut. The second, which serves as the final boss, is a gigantic purple dragon known as Jet Bahamut...which comes accompanied inexplicably by two other giant dragons, Garnet Bahamut and Amber Bahamut.
Crisis Core is quite possibly the hugest example of this trope. Two of the four main male characters become literal one wing angels -- one of which is black-winged and the other is white-winged. Then when you fight them they in turn transform into monsters, still retaining the wings.
There are even several varieties of mooks and monsters who have been infused with genes from those two and thus have a single wing sprouting from their back. The second half of the game feels like the monsters from the first half decided to reappear after having visited a grand Unpaired Attachable Wings clearance sale. It reaches a point where you expect everything that isn't a robot to have a bizarre feathery wing graft. Ironically, the only character who you would expect to sprout a wing doesn't in this game -- Sephiroth.
In the Dissidia Final Fantasy games, every character has an "EX Mode", and for many of the villain characters, it's their One-Winged Angel form. Kefka, for instance, gains his 'God of Magic' appearance, and the Emperor assumes his 'Emperor of Hell' form. Ironically, as a result of loading issues, Sephiroth doesn't assume his 'Safer Sephiroth' form from his game, instead taking on his Kingdom Hearts single-black-wing look. Similarly, Exdeath doesn't use his Neo form as his EX Mode. Instead, it shows up as an alternate costume in the Prequel. Its default setting is based on artwork - when it goes EX Mode, its colours change to match the actual game sprite.
And then, since Chaos is now his own character and not just Garland's transformation, he too gets his own One-Winged Angel form. In fact, he gets two -- during "Utter Chaos" he changes color and goes to huge proportions, then in Dissidia 012 an Alternate Universe version of Chaos goes berserk and insane to become Feral Chaos.
In Dirge of Cerberus Azul, one member of the Super SoldierQuirky Miniboss Squad is on his own a pretty large bruiser who hefts an assault cannon, but on top of that he can turn into a literal Behemoth for extra headaches. And unlike traditional Boss Encounters, he can switch between them at will.
The original Final Fantasy Tactics's entire villainous cast did this, with a Zodiac theme, giving at leastsixOne-Winged Angel forms The final boss does this as well, in typical Square fashion.
In the final battle of Final Fantasy Crystal Chronicles The Crystal Bearersthe big bad fuses with an airship and transforms the ship into a giant red crystal. At the same time the main character follows this trope more literally when his telekinetic powers manifest themselves as a blue surfboard thing, some sort of face guard and a giant blue wing.
Sheex, Fahna and Thanatos all do this in Secret of Mana. Geshtar might also qualify since his boss form, though clearly humanoid, is classified by the game guide as being robotic.
All the Bosses in the Romancing SaGa Trilogy had this: Romancing SaGaSaruin had 2 forms: His second being his upper half of his body sticking out of a sphere while he grew extra appendages to his torso and back (in the remake anyway). Romancing SaGa 2The 7 Heroes gradually joined the amalgamated form every 6,000 HP dealt.Romancing SaGa 3The final boss: Destroyer changes to a more crazed, shinier form with more wings that could also change into four other forms representing the four Devil Lords, but only if the form chosen was that of a Devil Lord not defeated. The protagonists can transform too.
Ah, Kingdom Hearts. The fight against Ansem has multiple phases, but he doesn't actually transform until you reach part 4 of the fight. Departing from the usual thing with bossess transforming, people tend to find his form when he first possess Riku harder, and his final form to be a pushover.
In the second, Xemnas fights you as himself, as a spaceship, as a suit of armour with a BFS, as a suit of armor again this time hurling everything he can at you (including the landscape), then himself again with different powers and a zebra suit.
It also features quite a few of Disney's One Winged Angels, notably Maleficent and Jafar.
358/2 Days brings us a One Winged Angel form for Xion. It's...rather difficult to describe...It's sort of like an armored monstrous Nobody form of none other than Sora. Interestingly, this is the form the boss assumes for all four phases of the fight, with each phase bringing new weapons rather than new transformations and the final phase bringing a bit of a growth spurt too.
Birth By Sleep notably doesn't do this. Every character's final boss remains human. Vanitas simply takes off his helmet and pulls out a different keyblade for his 2nd stage; Master Xehanort migrates into Terra's body, with the player taking control of Lingering Will for his 2nd fight; Terranort, the True Final Boss, simply summons Xehanort's Guardian familiar from Kingdom Hearts for his last battle; and for Aqua's story, the final bosses are two different characters.
In Super Mario RPG (co-developed by Squaresoft), Final Boss Smithy gains several forms after fighting with it once. The first looks like an evil bearded robot with a hammer. The second is the same robot, except with a giant skull for a head which can be switched to four alternate forms.
Also, the Czar Dragon turns into Zombone.
Seiken Densetsu 3, all 3 of the final bosses transform into giant monsters before you fight them. One of them has two forms you fight, though to avoid scarring anybody, his two forms collectivily about as much HP as the other two bosses.
Likewise in Secret of Mana, only you never fight the human bosses in their normal form; instead they tend to go One-Winged Angel right from the start. Even Big BadThanatos ends up becoming the Dark Lich for his fight.
Chrono Trigger contains at least four instances of this, in various forms: Masa and Mune combine to form a hulking beast, Queen Zeal becomes a giant, crowned mask and gloves with increased magical power, and Lavos does it twice.
The 'Dragon of Fire' fight in Chrono Cross. While the first time you fight him he's fairly small and humanoid, partway through the second fight he will change into an even larger (and cooler) dragon in the style of muscle growth.
Happens again in Cross to Dark Serge/Lynx, who transforms into a bizarre-looking giant purple humanoid embedded into the floor.
Parasite Eve has this for Eve, the main antagonist. She starts off by possessing the body of a woman, changes into a slightly disturbing form by having a giant fin instead of feet, long arms with sharp claws, and crazy hair. By the time you see her near the end of the game, she becomes a multi-breasted bloated monstrosity as she prepares to give birth to the Ultimate Being, which changes slightly when you fight her for the last time, but she also changes form from here by becoming an almost angelic figure once her HP gets low enough.
The protagonist accomplishes this as well in the first game, with her ultimate attack(of the two pure attacks in the game)'Liberation', the form being angelic, but in a biological manner. And the 'secret boss' from the first one manages the -same- form. Only she remains in it throughout the fight.
The sequel also has the final boss look and fight in a similar way as Eve's final form from the first game.
Guildenstern in Vagrant Story is a textbook example. He turns black, spouts wings, merges with the game's main religious symbol to turn into a giant cross-shaped... bug... thing, and flies around casting things with names like "Judgment" and "Bloody Sin".
The World Ends With You beats Sephiroth out in both religious symbolism and overkill on its Final Boss forms for its Big Bad: He turns into a giant serpent and then fuses with Joshua who was making some sort of cross, after which he turns into a five headed dragon that takes up the majority of both screens while holding your other two partners in his claws. In fact, most of the bosses turn into Noise during their boss fights.
It's a tradition in the Dragon Quest series for the final boss to have more than one form, starting with the Dragonlord/Dracolord/King Dragon in Dragon Quest I. To date, the only two final bosses in the series that don't follow this trope are Malroth in Dragon Quest II and Zoma in Dragon Quest III.
Special mention must also go to Dhoulmagus of Dragon Quest VIII, who is a mid-boss who does this.
A particularly odd case was the final boss of Dragon Quest IV, Psaro the Manslayer, having discovered the secret of evolution gradually loses body parts in the first half of the fight, then grows new limbs, ending with a completely different form from his first, which was itself completely different from his human form, and eerily similar to a previous boss, complete with new battle music.
Loki goes into One Winged Angel mode before he fights Lucian, and then again during the A ending events, you never get to fight his original form though.
In Bahamut Lagoon, Alexander does this. He's already a massive dragon by default, but after killing him, a dozen of the creatures that are used for vessels of reincarnation for dragons rush into the room. He ends up coming back as a multi-headed monstrosity that takes up half of the map.