Applied Phlebotinum - You need some form of explanation for why they're using giant humanoid robots/golems/biomechs instead of tanks and planes. It can range from "Getter Rays need a human form!" to "They're maaaaagical" and even more 'realistic' explanations such as Gundam's "Humanoid robots can turn around in space without wasting fuel". Careful with making these mecha more specialized - they may slide out of your series' focus.
Rule of Cool - Even the most Real Robot show operates on this, because if it were any more real, it'd just be using tanks instead.
Real Robot or Super Robot? - Do remember that Real and Super are adjectives, and not strict delineations of genre; nor are they Power Levels. Super robots can have numerous weaknesses and drawbacks to usage, and real robots can be extremely powerful (ever hear of nuclear weapons?). They are best defined as settings.
Real Robot: Gundam is perhaps the archetypical example of the Real Robot setting, with Armored Trooper VOTOMStaking it tothe max. Real Robots settings typically have the mecha as mass-produced weapons of war, and oftentimes they're ignominiously blown away, much like soldiers in war films. See also Patlabor, an even more realistic series given that it's in a non-military setting.
What do your mecha do? Do they fly? Are they speedy and lithe, dancing pirouettes around bewildered tanks and infantry, or are they clunky and landbound like BattleTech or Fang of the Sun Dougram? Are they mostly for space, like Gundam and Jovian Chronicles, or do they fight on planetary surfaces?
How large and mighty are your mecha? How powerful are they relative to other kinds of prominent fighting vehicles?
What kinds of technology are used? Just slugthrowers and sidewinders? Frickin' Laser Beams? Laser Blades? Cloaking? Funky mind control interfaces? Techno-organic building combiners?
Rule of Cool - What if the ultimate attacks are Awesome but Impractical? What if the heroes can win by being sensible and practical, reigning in their Hot Blood? What if the bad guys are the ones who do things just 'cause they're cool, while the heroes take these life-or-death battles more seriously?
Gundamjack / Black Box - what if whoever makes the Super Prototype / advanced technology in question had the foresight to take out a patent on the design, making it worthless for reverse engineering purposes? Sure, it's just silly in war story (why would people on the opposite side of a war would care about patent laws, especially if one side are aliens?), but can be done on smaller scale, like corperations conflict.
Space Runaway Ideon - Directed by "Kill'Em All" Tomino, who lives up to his nickname here, it is about the Ideon, a Super Robot with a rather scary power source, the Ide. Was one of the inspirations for Evangelion.
Armored Trooper VOTOMS - Votoms is the leader of what defines 'Real Robot'. The mecha are basically glorified humanoid tanks, and their main propulsion most of the time are wheels built into their feet. Instead of a kid, the main character, Chirico, is a hardened elite soldier who knows what he's doing.
G Gundam - a great example of how Humongous Mecha can be combined with any genre. A Chinese martial arts adventure with giant robots? Awesome!
Giant Robo - Both an old live-action series (with Giant Robo being a guy in a suit) and later an OVA series, which was directed by the same director who did G Gundam.
Neon Genesis Evangelion - Love it or hate it, Evangelion changed the genre forever. It created a whole new school of more organic mecha design, and subverted so many Super Robot tropes. It is the Watchmen of mecha anime.
Gundam Wing - The first Gundam series to gain a major fanbase in America, and in both countries, it introduced a new viewer demographic: Girls.
Eureka Seven - the genre with its most badass action, greatest character development and one of the most excellently handled anime love stories of all time.
RahXephon - At first glance, it seems to be an Evangelion imitator, but it's actually a Spiritual Successor to Brave Raideen. It combines a musical motif with mesoamerican mythology to create a rich, alien atmosphere.
Tengen Toppa Gurren Lagann - in case you don't want your Super Robot to fight one Monster of the Week after another, you can turn to these for good examples of lighthearted Super Robot adventure series. Gets darker later on, though also more awesome.
Fafner in the Azure - Though it starts off fairly slow, it's well-paced afterwards, and uniquely the focus is not entirely on giant robot battles. If Neon Genesis Evangelion is too disturbing for you, this is a more stable and melancholic alternative.
Gundam SEED- Say what you will about its sequel (see below), Seed repopularised the Gundam franchise and brought in a whole new generation of fans to Gundam. It also adapted parts of the original Mobile Suit Gundam storyline, while still managing to tell an original story with likeable, sympathetic, and above-all, well-developed characters.
Gundam 00 - This series subverted or outright avoided many Gundam tropes and developed the Political aspect a lot.
Macross Frontier - Took Macross to a whole new level. Just make sure you don't get your Humongous Mecha series in a sticky legal situation with American distributors though. Harmony Gold is notoriously responsible for preventing this series from reaching American shores.
Gundam SEED Destiny ... it certainly has a huge hatedom. If anything, it's greatest failure(s) seem to lie in the fact that all too often, personal conflicts between cast and crew would spill over into the story itself. Whether you like this series or not, don't let this happen.
Super Dimension Cavalry Southern Cross is not really spectacularly bad so much as uninteresting to the point of being a cure for insomnia. Reportedly, the Japanese reaction to the "Southern Cross" segment of Robotech was along the lines of "How the hell did they make Southern Cross watchable?"