Monkey Island: Guybrush Threepwood, when he's not being saved by Elaine or showing occasional random intelligence.
Jimmy Hopkins from Bully may be a subversion. Possibly just Brilliant but Lazy as he does have the intelligence to ace every class as well as the charisma to score with every girl (and a couple of guys) in school. Although he seems to wise up as the game progresses. Russell is a straight version of this, after his Heel-Face Turn.
Lloyd from Tales of Symphonia, who really takes the Idiot Hero → Fool → Messiah evolution to a whole new level of exaggeration, insofar as he actually sprouts wings near the end of the game.
Subverted. He is absolutely Book Dumb, but he is very competent when it comes to crafting. As the game goes on, he proves to be a competent leader and other characters sometimes remark that he's better at making quick decisions than them. Some of this is Character Development.
Tales of the Abyss protagonist Luke fon Fabre. Although he becomes a better person after his Important Haircut he still has plenty of moments that prompt someone, usually Tear, to tell him that he's an idiot.
It should be stressed again - Luke is mentally seven years old, due to the whole Cloning Blues thing. When you see it from this perspective, he's quite smartfor his age.
Further subverting Luke's Idiot Hero status is the fact that, in addition to having to learn everything from scratch over the past seven years (including walking, talking, and the faces of his family) he spent the entirety of those seven years being locked in his mansion with his family, closest friend and beloved teacher doing their best to keep him from getting any info about the outside world, ostensibly for his own security but actually because they're either plotting to eventually trick him into being a suicide bomber, kill him and his family, or both. Seriously, can you blame the poor kid?
But before that, Tales Series has its own first Idiot Hero in form of country-bumpkin Stahn Aileron. His genes of Idiot Hero is passed down to his son Kyle Dunamis.
Reid from Tales of Eternia as well, but that's mostly in the first half of the game, where his stomach is bigger than his brain.
Adell from the second Disgaea game. Adell is far from an idiot in most matters that don't conflict with his Honor Before Reason out-look on life... but — as noted by Rozalin in the page quote — having that outlook seems practically suicidal, given that he is the only human left in a world overrun by demons. This makes him both a perfect, defining example of this trope and a subversion of it at the same time, if that makes sense. He has proven capable of providing great insight, and can solve complex Geopuzzles within seconds without even thinking too hard, which astounds his most recent friends (who thought of him as a more archetypical idiot). He even lampshades this himself a few times: it's not that he doesn't see the problems with his approach to things, it's that his code of honor won't let him do anything other than formally challenging his enemies head-on, so he puts those problems out of his mind and proceeds on faith. Also worth noting is that Adell is the Only Sane Man of the game, and he knows it.
Axel plays it straight in his storyline in Dark Hero Days.
Junpei Iori from Persona 3. One of the rare non-central protagonist cases. He tends to make up for his idiocy with pure heart, but not always.
While Junpei displays astounding levels of Book Dumb, he straightforward approach to problems usually gets him through. However, he displays some truly amazing (for him) insights into situations and people that imply he might be smarter than he looks.
Atsuma from Enchanted Arms. An especially bad case in that he has to be taught how to, among other things, use ladders and swim across shallow water. To his credit, he does get the hang of swimming right away, but still...
Beat from The World Ends with You. Example: After discovering a box with a button on it, Beat happily presses it, despite knowing it was left by the main antagonists. Neku puts it best when he says "I think they design traps like this with you in mind."
There's also the manner of his death, when he tried to save his sister from a speeding car by jumping in front of her to shield her from the impact. Even he admits that this one was pretty stupid.
Roger Wilco from Space Quest isn't the sharpest tool in the janitor closet. The only reason he manages to momentarily escape his janitorial vocation in Space Quest 5 is because he cheats on a test and a mouse chews up the wires in the test's scoring computer. Still, the guy managest to step up to the plate and save the galaxy more times than he's had showers because he has the Indy Ploy down to a science.
Roger's stupidity suffered from Flanderization starting in the fourth game. Prior to that, he wasn't so much stupid as lazy and incredibly ineffectual at his job. It's only when he steps outside his job description that he really shines, though his janitorial skills do come in handy at times.
Bartz's personality is actually somewhat more defined in Dissidia, where he is portrayed as a guy that can find the fun in any situation, and gleefully does. This doesn't make him take a given situation any less seriously, he just likes to put a positive spin on it. Sometimes to the point of idiocy.
Zidane: Bartz, do you even have any idea where you're going? If you only focus on what's right in front of you, you'll never see the route ahead! Bartz: Eh, I don't mind a little aimless wandering. In fact, it's what I do best! Besides, since there're all these guys trying to stop us, we must be going the right way! Zidane:...Is this guy for real?
Vaan: We just came from there. We need to go this way.
Laguna: ...I knew that. Just testing ya.
Tidus' unfamiliarity with the world of Spira (although he has a good reason) and his relentless cheer (not as good) made an Idiot Hero out of him for a good portion of the plot. At least, until The Reveal of Yuna'sPilgrimage made him realize the seriousness of the situation.
Lyner Barsett of Ar tonelico, in both general intelligence and romance. In an early part of the game, upon being told by a companion that he will have to learn Item Crafting to defeat enemies immune to physical attacks, he protests, "But I can do it if I just put my spirit into it!" In keeping with the trope, he becomes a All-Loving Hero by the end of the game, having united the world's various divided factions he's met throughout his journey and convincing Mir to give up her plans to Kill All Humans.
Yuna Kagurazaka, lead character of Galaxy Fraulein Yuna. In the first game, Elner is frequently chiding her for getting distracted or not using her head; Yuna mostly matures out of it later on.
Edy Nelson from Valkyria Chronicles is this, surprisingly enough. In her DLC, she and a small detachment get separated from the squad because she went Leeroy Jenkins on the Imperials. As it turns out, most of the squad were scattered, so Welkin orders all those separated to regroup, but when she heard that Imperial forces were attacking a nearby village she tells the group with her to attack, ignoring the fact that the enemy has tanks and their group only has Jann. Later, she hears that Rosie got shot so she ran across the battlefield just to make sure she's okay, afterwards claiming that she did that because she can't let anything happen to Rosie until she surpassed her on the stage.
The hero of the sequel, Avan, takes this to Up to Eleven levels in that he scored a negative ten on his last exam, according to his backstory. In fact, he's so stupid, some fans have begun theorizing that he's batshit insane.
While we're on Mana Khemia, Ulrika from Mana Khemia 2: Fall of Alchemy fits this trope even better, especially intelligence-wise. At one point in the game, Ulrika takes a look at little Enna's lesson book and she doesn't understand a single bit of information written on the book, much to Enna's and Chloe's shock.
In spite of the quote above, The Legend of Zelda's Link is a subversion when he might appear to qualify at all: while there's plenty of swordplay in Zelda games, the meat of the experience is puzzle solving, whether getting past obstacles or figuring out the trick to the Boss Battle.
The fandom loves to portray Mario himself this way.
There are idiot heroes, and then there is Ethan Kairos of Time Hollow. When his friend Morris tells him of a book about parallel universes that might greatly inform his current predicament, Ethan thinks about it for a moment - then decides he can't be bothered to retrieve it from their clubhouse and wants to go to a nearby antique shop instead. He routinely, stubbornly refuses to acknowledge the blindingly obvious and just as often fails to do anything to follow the leads that are actively handed to him. He's also a bit of an unlikable prick.
Fallout and Fallout 2 were filled with conversation options to allow for the player to be the Idiot Hero, and you can even lower your INT below 4 and have your character be mentally retarded. While Fallout 3 didn't have this option, Fallout: New Vegas writes it back in (possibly owing to the fact its developers include Black Isle refugees and thus are fond of making throwbacks to the first two games), albeit in a somewhat more limited degree than its predecessors.
In New Vegas, having an extremely low Intelligence score causes your character to literally be a barely functioning retard, unable to speak proper English ("I is scientistic.") and it actually makes the game easier at some points (for instance, Arcade Gannon will join you, since he feels sorry for you). While possible in the earlier Fallout games, your character will not be able to do the majority of side quests.
Likewise Arcanum. 'Idiot Savant', 'Frankensten's Monster' and 'Bride of Frankenstein' backgrounds allowed for a subversion, highly intelligent characters with total communication incompetence.
In Atelier Annie, while he is obviously not the hero of the story, Kilbert is a send-up for this character type.
Spinoffs aside, the only playable character from Touhou not to have some degree of this is Sakuya. Youmu would be a fairly archetypal example except she's not the main character. Reimu is the main character, but lacks most of the positive qualities associated with the trope. Marisa has the basic personality, but is actually fairly clever and knowledgeable (despite openly claiming to be stupid). And Sanae is an airhead. Including spinoffs, Cirno acts the part fairly well, but she's only good at combat relative to other fairies.
Rayman seems to fit this trope in the upcoming prequel Rayman Origins. He was also a bit of a Cloudcuckoolander in the original game.
Battleblo from Cla Dun: This is an RPG! His goal in life is to seek out the "ultimate shield" so that he can defeat his rival Sunday, an Action Girl in search of the "ultimate sword". In-story, he uses shields as a means to solve all of his problems.
Kirby, a Cloudcuckoolander in his own right, is quite fond of being an Idiot Hero as well, simply because there are some times where he goes around in a quest to solve a problem whose real source he doesn't know anything about. For example, in Kirby's Adventure and its remake, Kirby: Nightmare in Dream Land, he thinks King Dedede tried to mess with everyone's dreams by stealing the Star Rod from the Fountain of Dreams, breaking it apart and giving each of its seven pieces to one of his friends, but he doesn't know that Dedede was actually hiding it safely away from the real culprit responsible for the problems in Dream Land, a vampire-like wraith called Nightmare who rode the currents of the fountain, wreaking havoc and tormenting Dream Land's citizens.
Also, there's Kirby Squeak Squad, where he chases after the Squeaks thinking they stole his strawberry shortcake. But Meta Knight knows the secret of said treasure chest that Kirby doesn't know about - the chest is the prison of Dark Nebula, the ruler of the underworld (Lord of Darkness in the Japanese version). Hence, why Meta Knight snatched the chest before Kirby could take it back from Daroach.
Ragna the Bloodedge of BlazBlue is, as his stalker Rachel says, quite a moron and as foolish as always because he has a foul mouth and curses too much and has a tendency to run headlong into trouble. He has quite an "I will do what I want" attitude, and when other people try to convince him to refrain from trying to do what they think is impossible, he refuses to listen and just keeps on going - because he never gives up, no matter what the future has in store for him.
This saves his life when he fights Arakune. Arakune usually eats his defeated foes... but he passes up Bang because he thinks devouring an idiot will endanger his quest for knowledge.
There's also Taokaka who is a borderline The Ditz. She can't understand longer words, often forgets things after a few seconds, and when she attempted to go bounty-hunting for Ragna, she ended up befriending him just because he bought her some food. She also humorously doesn't get that "Rawrgna" and Ragna are the same person.
Ladies and gentlemen, we have the reigning queen of stupidity: surprisingly enough, Spiritia Rosenberg of Rosenkreuzstilette. She has quite the long list ahead of her. For starters, being an Expy of Mega Man, she is naive, as pointed out by her colleagues (some of them even think her naivete could be her fatal flaw) - naive enough to believe that Iris really is a kind, innocent girl who wouldn't even hurt a flea. When her friends at RKS start a war against the Holy Empire, she does the whole "Swiper, No Swiping!" deal with everyone without knowing that Iris actually started the war between both factions just For the Evulz and without snooping around to get to the bottom of the madness (at least she does what she thinks is right). And then there's the moment in Rosenkreuzstilette Grollschwert where Tia tries to stop Grolla from killing Iris herself believing that she was a sweetheart. Grolla knows otherwise from her own personal experience. And, to top it all off, she is quite clumsy and is a TERRIBLE swimmer. Yes, you heard us. A TERRIBLE SWIMMER.
Sepperin: (To Tia) Hmph. Such naivete. You are still a child, after all...
Mortal Kombat gives us Shujinko and Taven, both of whom were exceedingly gullible. At least in Taven's case, he has the excuse of being a case of Sealed Good in a Can, awakening in a different realm after thousands of years of rest, and being attacked by everyone, including other heroes.
Amitie "Amita" Florian of Magical Girl Lyrical Nanoha A's Portable: The Gears of Destiny, who seems to have watched way too many Super Robot and Toku shows and believes that the only things you need to succeed in are Fighting Spirit! and Guts! and Hot Blood! Among other things, she accidentally causes a lot unnecessary confrontation with the older characters by pointing her guns at them at the beginning while asking for their help, gets immediately distracted when confronted by Arf because "Squee!~ Dog girl with dog ears and tail", and refuses medical attention for a virus because she states that Fighting Spirit and Guts are all you need to overcome. She also believes that she's a Super Hero, though she's more right about that last one since she's a Ridiculously Human Robot from the future who fights for her planet.
Ratchet from Ratchet & Clank has his moments. Notably in R&C5 when Ratchet is completely confused as to why Luna has a latch on the back of her head with monitors and Technomites inside.
Clank: Ratchet? Do you notice anything strange about Luna? Ratchet: Well, she does seem to have an unusually large door on the back of her head. Clank: And why do you think that is? Ratchet: Because she's a... uhm... robot..?
Averted wholesale in Xenoblade Chronicles. The protagonist Shulk is actually quite intelligent, but is inexperienced. Even Reyn, who would normally be next in line for the title, is well-spoken and capable of reasoned debate. You can count the total moments of protagonist stupidity that aren't due to misinformation or traps on one hand.
Commander Shepard from Mass Effect often came across like this especially in the first game because he/she was given the role of the Audience Surrogate and continually asked questions that should've be common knowledge to everyone in the universe. Later, s/he comes across more like a Genius Bruiser.
The Avatar in Ultima IX comes off as this, being told "Your knowledge of the land shall be great", but he has to be reminded of stuff that had already happened. Taken to Memetic levels when he asks, "What's a Paladin?"
Thanks to Sequence Breaking (And the devs anticipating overleveled players skipping quests) you can say, ask "What's that creature type?", "What's going on in this world?", or "Who is this faction?" when a previous quest briefed you of such things.
The Evil Plan of The Foundry flashpoint is to destroy anyone with Sith DNA in them, which encompasses 99% of the Sith Empire. The player characters are able to say "Well, guess I should feel lucky" or "Good thing my species doesn't have any Sith DNA in it". What makes this most amusing is the fact that Sith Pureblood characters can also say this.
The Adventures Of Massmouth: Massmouth doesn't seem to be very bright. Especially visible in Massmouth 2, where most of his lines are basically variations of "what?" or "uh?"
Pixel from Graffiti Kingdom. Good lord, just check out his quote on the Quotes page!