Phoenix Wright: Ace Attorney has a number of these characters, to the point where your average ditz nearly always is smarter than they look.
In the original game, the supposedly beyond-senile Yanni Yogi (a Shout-Out to Yami Yugi) faked permanent brain damage for fifteen years before trying to exact revenge and get away with it.
Case 5, in the DS remake, has Police Chief Gant. His guise of a lovable, laughing buffoon hides not only a razor-sharp mind, but his true personality of a ruthless genius willing to kill one of his own officers, and blackmail another by framing her sister, in order to put away a serial killer.
In Justice For All, Ini Miney from case 2 and Matt Engarde from case 4 are both smarter (and more sinister) than they appear to be at first glance.
In Apollo Justice: Ace Attorney, Phoenix Wright himself shows a bit of this trope.
Done in Ace Attorney Investigations with the ditzy bubble-blowing Cammy Meale, the jovial Ernest Amano, and the elderly Quercus Alba. They're all murderers or accessories to murders, and all work in the same smuggling ring. Since veteran players of the series will know to look for the trope, the game even plays with your head a little with the delightful, energetic, and oblivious Colias Palaeno—who never even comes under suspicion.
From Dual Destinies we have detective Fulbright (aptly nicknamed Fool Bright by prosecutor Blackquill). For most of the game he looks like a regular detective who strongly believes in justice. It turns out he is actually a spy who killed the real Fulbright, Metis Cykes (Athena's mother) and Clay Terran. He can also hide and pretend emotions (almost) perfectly.
When Raven joins your party in Tales of Vesperia, he presents himself as a goofy but skilled middle-aged Handsome Lech who imparts nuggets of wisdom that no-one asked for and constantly complains about how he can't keep up with the other, much more youthful party members. In fact, he's The Mole for the local Smug Snake. His true identity is that of a cunning, experienced and suave knight who, under his "Raven" persona, managed to infiltrate the highest levels of the Dahngrest government over ten years.
Arguably, the entire Team Fortress 2 team, all of whom the Announcer refers to as having "below average" intelligence, outside the attack classes, could count. Demoman seems like a friendly, reasonable guy when he's not drunk, based on the War update comic, and it's hard to be stupid and make five million dollars in one year. Heavy has a Ph.D. in Russian literature, and if the Russian "Meet The Heavy" is any clue, is much more eloquent in his native language. Engineer has 11 "hard science" Ph.D.s, which speaks for itself. "Meet The Medic" revealed Medic is indeed a trained doctor, though he's barking mad and he lost his license for stealing a patient's skeleton. Sniper managed to rig a tribal shield to electrify its attackers, and while not as smart as the rest, doesn't seem "below average." Spy had the resources, intelligence, contacts, and capability to thoroughly research a "Your Mom" joke, in addition to being able to do a spot-on impression of the voice of all eight other team members, and seeming like a completely civil, intelligent gentleman off the battlefield. Below average, indeed.
Pyro could be too, as most of when he/she's trying to speak under the mask sounds somewhat condescending.
The recent 'Meet the Pyro' video revealed that the he is utterly insane and views the world as a happy, colourful place where she skips around dishing out lollipops and rainbows to adorable cherubs, where in reality it is causing pain and suffering by shooting gouts of searing flame at his enemies. Since she has such a warped view of reality the smart/dumb scale doesn't really apply to it.
It's his goggles that make the world trippy, not he/she/it. And if even if he/she/it is crazy, it's fair enough as he/she/its been forced to look at a ridiculously happy world for god knows how long.
Really, none of them could be below average, they just appear dumb to the Announcer.
Levin from Soul Nomad & the World Eaters appears to be a complete idiot...up to the point where he stabs your Old Master dead out of the blue and reveals he's the last world eater; he's helped you because you've been killing off — or given him an opening to kill — everyone who was ever a challenge to his future bid for godhood, and every single time he left the party to wander around and came running back dragging trouble behind him, he did it entirely on purpose.
Resident hungry ghost Yuyuko Saigyouji, of Touhou, definitely fits the bill. It's even a possibility she's actually even smarter than The Chessmaster Yukari.
During her appearance in Imperishable Night she keeps talking about the incident-solving as a "wonderful midnight snack tour across the land" and have an overall very carefree attitude towards the whole thing. But if you look at her dialogue carefully, it's very much implied she already figured out everything beforehand, and each "dish" is a metaphor for every enemy they're facing.
She continues this in Ten Desires. After picking a fight with the player character for no real reason, she then quickly points them out to the right direction despite never actually leaving her mansion.
In the Sinnoh region of the main Pokémon games, Dr. Footprint can essentially read Pokemon's minds. Some of the more slow or dumb Pokemon will express simple thoughts full of "hnurr" pauses - except when they suddenly share a complex and grammatically correct sentence or two about how people and other Pokemon assume that they don't think much because they don't speak up often. They don't seem annoyed or insulted though.
Shuji Ikutsuki relies heavily on this to fool Persona 3's protagonists into bringing about the Fall for him. A harmless character known for bad jokes becomes The Chessmaster in one fell swoop..
And in Persona 4, Adachi plays much the same role. People who have played Persona 3 will probably be instantly suspicious towards him because of it.
Actually, a video of Ikutsuki in FES shows that he genuinely thought those jokes were funny, so it's more of a subversion.
Dark Adonis aka Midboss and Seraph Lamington from Disgaea. The first appears to be a foppish Recurring Boss whose sole purpose in the story is to get his ass kicked by Laharl. The second appears to be a hands-off sort of boss content to just walk around his garden while his subordinate plans a coup to conquer reality. In the end, it turns out Lamington was aware of everything all along. In addition, the entire game is essentially a Secret Test of Character masterminded by Lamington and Midboss to make Laharl a great and compassionate Overlord. Midboss is also heavily implied in the end to be the temporarily reincarnated form of Laharl's father the previous Overlord.
Asmodeus from Painkiller, an easy-going imp who followed Daniel around for most of the game only to reveal that he was Lucifer himself, digging holes to allow demons into Purgatory from Hell.
He's smart enough to have conquered half of the world in his ending at the very least.
Knox Harrington in Vampire: The Masquerade – Bloodlines first appears as a vampire's excitable, none-too-bright servant who's gotten in over his head while following a target and needs the player character's help. Turns out with the right questions and mental stats (or Malkavian insight) that he's actually a competent former bounty hunter and his job all along was to get your character to go after the target.
Double from Mega Man X 4 is a portly rookie Maverick Hunter, who is shown falling over at times in the game's FMV. Despite his goofy appearance and clumsiness, he is actually a fiercely powerful reploid in a fake body
No One Lives Forever has a recurring character - a drunk who shows up in virtually every level, acting like an idiot. He even somehow shows up on an enemy space station, presumably just for the gag...but a post-credit sequence reveals that the idiot is actually the leader of HARM, the evil organization, spying on you personally
The main character of Devil Survivor has some decidedly ditzy dialogue options (especially: "What's 0+2?"), but generally seems to figure things out much faster than he lets on. He even gets called out on it in one of the Multiple Endings.
It gets Lampshaded earlier than that, too. In the game's prologue, during a brief meeting with Naoya, the main character has the option to guess that the Laplace Mail is predicting the future. Naoya is amazed — not just because that's correct, but because it's a downright bizarre and even somewhat stupid conclusion to draw from the current evidence.
In The Force Unleashed, after losing his eyes, Rahm Kota becomes so depressed that he spends all his time binge-drinking and claims that he has lost his connection to The Force. It eventually proves that he is still a mighty Jedi Knight, like when he steals Emperor Palpatine's lightsaber.
Though, then again, that happened AFTER his He's Back moment.
Played straight and averted in Arcanum: Of Steamworks & Magick Obscura. In the Museum of Oddities in Tarant there is an exhibition of Gar, "world's most intelligent Orc". It turns out that Gar is actually a full-bred Human with a strange mutation and just pretends to be stupid, because people wouldn't put up with an Orc smarter than themselves.
It's very debatable as to whether Space Quests Roger Wilco is a lucky Idiot Hero or brighter than he looks and just very unmotivated. The Big Bad of the sixth and final game muses about this and concludes it's some of both.
Gaston is Luminous Arc 2 is such a Large Ham his overacting gets questioned by other characters in the game on occasion, but has a very real, very sensible code of honor and duty to the Queen, and is a legitimately skilled Knight Commander, preferring to lead from the front line.
In Dragon Age II the Hawke's "sarcastic"-choice dialogue indicates that personality type uses this and Buffy Speak seemingly as a tactic to lure enemies into a false sense of security, before revealing that their title of "Champion of Kirkwall" is very much deserved and they really are that dangerous. Cue many an Oh Crap moment from their enemy.
Sarcastic!Hawke: Oh I'd make a terrible slave. For one thing, I talk too much.
[pulls a knife out thin air and holds it to the slaver's throat]
Sarcastic!Hawke: Plus, I do that.
In the original Dragon Age, take a shot every time someone mentions the old saying that Mabari are clever enough to speak and wise enough not to.
When reminded in the endgame that the other Wardens will have questions about the Archdemon and why both Wardensmade it out, Alistair cheerfully replies that "I can shrug and look stupid. It's a talent." (Alistair himself—despite what Morrigan insists—has a decent education as a Templar and is a competent soldier, and if he's hardened and made king, he does better at ruling than Anora (well, most people) imagined.)
In RuneScape, there's an NPC near the Barrows Brothers who is only known as the Strange Old Man. Normally, he just acts like a useless idiot who won't tell you a damn thing. But during the quest "The Temple at Senntisten, the Strange Old Man becomes a lot more lucid, a lot more direct, and a lot less weird.
Player Character: But I thought you were just some mad old bloke with a spade obsession.
Strange Old Man: I do my best to look useless. If only others knew the truth, it would chill their hearts.
Letho, the Kingslayer, from The Witcher 2. He's a big, hulking mountain of muscle who really doesn't look very smart and he uses this to his advantage like a true Magnificent Bastard as he manipulates the Scoia'tel and the Lodge of Sorceresses to aid him in slaying kings under the pretense that it would aid their own ends, when his actual goal is to make the Northern kingdoms descend into chaos so the Nilfgaardian empire could easily invade them:
Sile de Tanserville: Letho played us all! We were decieved by his dull face and sluggish stare.
Little Busters has Kyousuke and Masato. Kyousuke is naturally silly and childish, but Refrain reveals that sometimes he was acting that way to throw Riki off from considering his true motives by pretending he was just acting on his own whims. Likewise, Masato is kind of a Dumb Muscle, but he dutifully followed the script Kyousuke set for him to continue to act that way and pretend not to know anything Kyousuke was doing so as to uphold the world and keep Riki at ease.
Mad Father: Aya, concerning her father's experiments (at least at a young age).
Aya (in narration): I feigned ignorance the whole time. Because I loved father.
In Super Robot Wars UX, Richard takes up a foreigner act and starts talking mixture of easy words from languages to pretend he's not a serious mercenary when he's on cover missions with Saya, Agnes is completely fooled by this and thinks they are comedians (comic story tellers).