Skull the Troll from PvP is a textbook case. Normally child-like, naive, and harmless, but deep down he is still a fierce mythical beast, whose more than capable of holding his own in an epic battle scene.
He's such a crouching moron, that while he's fighting the big bad, his own teammates assume he has run and hid.
Also more recently, he's shown catching a war hammer in one hand.
Gamzee Makara from Homestuck. He starts being introduced as the most useless of the trolls. But we later find out from references that in the trolls' final battle in their session, Gamzee did more damage to the Black King than anybody else, which shocked his teammates and their opponent. When he's cut off from his mind-rotting sopor pies, he also becomes sadistic, competent and utterly terrifying as he declares he will murder all his friends. He's off to a good start.
Then there's John. His most defining trait is his relentless optimism, which periodically leads him to do really, really stupid things on bad advice from complete strangers. He's easily distracted and tends to waste time screwing around reenacting scenes from terrible movies, losing computers, and literally bumbling his way to greatness. But get him really pissed off and he will use the Egbert family strength, a big hammer, and the powers of a wind god to wipe the floor with your arse.
Caliborn, in that he seems rather preoccupied with asking Derse boys to draw smut for him on introduction, and then goes on to overshadow the entire website.
Really, if anybody in Homestuck gives the impression they're a moron, expect them to be crazy powerful.
Gabe, from Penny Arcade while occasionally homicidal on his own, ups this to eleven when in possession of a certain cardboard tube.
Ray from Achewood happens to be the son of Ramses Luther Smuckles, an all-around badass and one of the most celebrated brawlers in American history. He enters the Great Outdoor Fight with essentially no training but manages to destroy a number of stronger men when his best friend Roast Beef is apparently in danger and his latent fighting instincts are aroused.
For example: during the GOF, another army leader (in the GOF, the first few days involve groups of fighters forming ad-hoc armies led by the most badass members) approached Ray at night, knocking him to the ground and calling him a coward and a liar. Ray's response? He ripped the dude's face off with his bare hands.
Arguably Liquid Snake of The Last Days of Foxhound also applies, considering it's been implied that despite his borderline idiotic behavior he is in reality a killing machine, but has lost the majority of his skills due to an accident caused by his overly aggressive behavior. He gets more intelligent as the comic moves closer to the events of the Shadow Moses rebellion of Metal Gear Solid.
Both Joyce and Walky from It's Walky! fall under this. Joyce in particular is ordinarily a complete innocent, with a passion for puppies, stuffed animals, and all things pink and frilly. However, if you push her just far enough... whoops, maybe that was a bit too far.
Big Boss: How's Joyce doing? Why has she made no progress? Professor Doc: Big Boss, we can't afford to fix her! Do you know how many times she's saved the world's collective ass with her psychotic outbursts? Big Boss: Three. Professor Doc: Well, I'm holding out for five.
Walky meanwhile is an excellent example that the trigger doesn't have to involve an immediate threat to yourself or your loved ones. This, for example, is what happens if you mess with his favorite snack food.
Grace from El Goonish Shive can best be described as a bubbly, naive girl, which would almost make you forget she's a genetically engineered Super Soldier who, the one time she actually got angry, proceeded to toss megalomaniac arch-villain Damien around like a rag doll, only to turn around at the last moment and ask him to forgive her.
This line from Raven perfectly sums her up:
She killed Damien. She could kill twelve Damiens. Those Damiens could merge into a super-Damien, and she could kill that. Provided, of course, that Damien did not do anything to startle her.
Mega Man in Bob and George. Ordinarily he's a complete buffoon. But when he goes into battle, particularly against the Robot Masters, he becomes Badass, often coming up with clever ways to defeat them. The fans figured out a reason for this, and the author said "Sure, Why Not?": In one of the early comics, the punchline is that Mega Man was accidentally programmed first to defeat evil robots, and second to be an idiot. He later retconned that this was the reason Mega Man was a default moron whenever there wasn't evil around, but when a bad guy shows up, he becomes an instant badass for the duration of the crisis.
Fighter: Cool. Because friends look out for one another and we're friends, but Black Mage is my best friend. Also, I can block any attack and kill anything that bleeds. Hint.
He once used his swords as chainsaws to destroy an entire flight of unstoppable dragons just because he was too stupid to realize said action was impossible.
Not to mention he once survived a fall of several thousand feet by blocking the planet before it hit him. Seriously.
Fighter: It's not the fall that kills you, but the ground. So I just blocked the ground.
Smoke from WTF Comics, starting as a little pocket Monk with seemingly no real battle capabilities besides dodging things, until Nikisha stabs Anna in front of him, and make him go "all out" in rage with annihilating an entire bridge of Mooks along with the bridge itself under them, nearly killing her too in the process.
Oh, and did we mention that he can also teleport, modify his own perception of time, resurrect the dead, and see the very fabric of the Timespace around him?
In a couple of Ctrl+Alt+Del comics starring the "players" (homicidal gamers with the tendency to carry out in-game vendettas in real life), Player 3 makes an appearance. He's normally laid-back and "normal", but can turn homicidal if threatened...
While lacking the Crouching Moron element, Lilah is notable for having insanely good game playing skills whenever she's really angry with Ethan.
Xykon in The Order of the Stick. He's funny and a fan of what one might call "Leeroy Tactics". However, if you challenge his reputation, he'll smash the whole ceiling on you. And gods help you if you lose his phylactery...
Ah, but he's a Ditz with a firm grasp of "bardic tradition," so much that he has accurately predicted future events based solely on how good a story they'd make.
The Monster in the Dark is also a nearly textbook example. He's pretty much a moron (although he has been thinking a bit more lately since his friendship with O'Chul), and a Minion with an F in Evil, but he's been shown to actually be ridiculously powerful, to the point where stomping his foot causes a major earthquake.
Redcloak most of the time plays Xykon's chief minion. Tsukiko considered him an easily cowed malicious sycophant serving the lich and nothing more — despite being the prophet of the Dark One and whatnot, but she's rather oblivious in general. When she really crossed him, Redcloak simply politely explained how much of an idiot she is, murdered her and told Xykon "I didn't think it was a big deal".
In The KA Mics, Gertrude and Brunhilda are normally comic bumblers, but when their sister was in trouble, glowing eyes and dead Mooks followed.
Torg, despite taking a few levels in badass over the years, is still mostly just a goofy, not-too-bright guy that everyone treats as pretty harmless. Probably best exemplified in this strip:
Riff:Dude! When did you learn to kick ass? Torg: I've been taking an Internet college correspondence course in kickass. Riff: You have not. Torg: But I so want to teach one!
Riff is a milder (or more complicated) example. He's superficially cool much of the time, but under that "strong and silent" act he rivals Torg in stereotypic male dumbness (and beats him in insensitivity); in the presence of the opposite sex, whenever he tries to do anything but look cool, he puts his foot in his mouth and becomes a total fool. However, he's right at home being a Bad Ass action hero or heroic leader when the right opportunity arises. So in this case you might actually miss the "moron" part of the trope if you only saw the superficial everyday coolness and the hero mode.
Dan's best friend, and the other half of the title, Mab, also qualifies, though for different reasons. She generally seems innocent-to-downright-nuts, with her main hobby being 'hugging things', feared mostly for her nightmare-inducing brownies...however, she IS a Fae, and resultingly, has god-level magical abilities - and when forced to use them, she can frighten ANYONE into submission - and then go right back to her perky, airheaded self again. Also, it turns out she's actually a Magnificent Bastard above all other Magnificent Bastards, plotting out everything, including the path that the Omniscient Council of Vagueness will take, in order to create the best possible future. She knows who will live and who will die. She just doesn't know how to bake.
By extension, this applies to pretty much the entire Fae race - Mab is merely the one most often found mixed up in the main plot. Being superdimentional beings of pure magic and/or insanity will do that to a race.
Biggs, the womanizing ferret who is more often than not bullied into submission by his sister Wildy might look as te most imcompetent leader of the Twink Territories... But he's still a leader, and if he needs to, he can get Dan's ass handed to him.
Ordog from Out at Home is a tiny, frail, senile old man who doesn't know where he is half the time. But he will kick your ass.
Diva Beelze from Evil Diva is kind of a little...silly, but she's pretty bad ass in chapter 2 in that she beats the crap out of the devil thugs without hardly doing anything. She has the super special wand but...so did Sailor Moon!
Sir Muir, a scarred old Darsai knight from the webcomic Harkovast appears to be a prattling, senile goofball when nothing exciting is happening. However he proves that he's quite a competent (though distractible) fighter when the situation calls for it.
Kharla'ggen from Drow Tales plays with rubber duckies and rarely, if ever, utters a complete sentence. Her guards barely care about their job. But she's the leader of one of the major clans in the setting and her laissez-faire rule is undisputed because she also likes to play with dolls. Her power is such that in a side-story she was able to 'play' with a greater demon, made of a composite of lesser demons, who collectively barely escaped with their lives.
May run in the family. Consider Donovan—a bard, prone to bad jokes and worse puns, horrendous at speaking Orcish (Or is he?), and by all appearances an utter goofball. He is also a world-class swordsman, helped save the world from a demonic invasion, and was one of the few humans to receive a tattoo from the orcs that basically translates as "The dude wearing this is freaking awesome."
Dave from Narbonic is the Butt Monkey and Unlucky Everydude for most of the strip's run, until the final few chapters where it's revealed that he's the most powerful and dangerous character in the whole series.
Tip from Skin Horse is generally considered the laughingstock of the eponymous organization - even next to a talking Canadian dog and a sociopathic zombie girl. Then he turns out to have gone through Afghanistan and have rescued three fellow soldiers from a burning humvee.
Those three Jägermonsters (Dimo, Maxim, Ognian) from Girl Genius known as Da Boyz. They're goofy, not overly bright, and have silly accents. But sooner or later something goes down, and the reader is sharply reminded that Da Boyz are SuperSoldiers, over two hundred years old, unwaveringly loyal to the House of Heterodyne, and quite capable of beating pretty much anything into a pulp.
Soul Symphony: What's the first thing John does when he wakes up in the Soul World and first learns about magic? He kills an enemy in one punch, and then kills six more using a basketball. This is before the protagonist managed to even hurt any of them.
Arthur Wight of Suppression is introduced getting ordered around by his daughter, who looks to be all of ten. He mopes, chain smokes, and trails around behind Maxwell, right up until he takes on Red Cerene and cuts her in half without once showing more effort than "yeah, I'm evil, cause...yannow."
Bill of Legend Of Bill is a wannabe barbarian hero with no actual fighting skills. Given that the strip is generally humorous, it's easy to assume that the title is a joke. Then this happens. And this.
Grymm from Voodoo Walrus tends to be light-hearted, silly, and more than a little oblivious to the world around him. But more than a few times he's switched to his badass alter ego of the Masked T-Square to take care of serious business. He also seems to be far more level headed and even uncharacteristically manipulative while portraying this character.
Though recently the creators seem to be pushing the idea that Grymm and the Masked T-Square aren't even the same person despite multiple past pages existing as proof.
Donald from Dark Legacy Comics is shown to be Too Dumb to Live and is completely useless at fighting (and pretty much everything). However during a Raid Boss the group had been stuck at for three months, Nyte whispered something that caused Donald to lose it and slice his head off in a single strike.
Donald: WHY DID YOU EAT SANTA YOU BIG BLUE MEAN FFFUCK?!
Mr. Fish from Manly Guys Doing Manly Things does it twice over. He's a Gyrados, and was Jared's worse-than-useless starter Pokémon when he was a Magikarp... right until he evolved, which is true to the original source material. After he's introduced though, he's not very bright, has trouble fitting in the corridors, and tends to eat people (including his trainer), but if you manage to get him to an actual fight, he will Hyper Beam anything in his way.
Jared: I didn't know... I didn't know he was a laser fish.
Jared qualifies as one in his own right. He raised that fish.
Jared Kowalski does not understand basic concepts, like Pokeballs. He raised a man-eating laser fish and got it to obey him, without understanding Pokeballs.
Mittens from Commander Kittystarts as a bumbling, oafish sidekick, but after getting "adopted" by Morris and subsequently getting a new outfit and some words of encouragement, he becomes the single most competent and Genre Savvy character in the comic, so much that Ace even begins to doubt his own effectiveness as a leader.
Jim Finn from Skin Deep fill this trope very well. He is a Tall, Skinny and laid back young adult with a long green air tat enjoy to play "Gorodove" (a wonderland card game), and is said to be even more eccentric than Merial. Despite this, it's worth to notice that Jim is actually a large griffin, more than capable to hold his own against the "Momo" (AKA Monster of Missuri), and even in human form, he's strong enough to knock out a demon with a single punch.
Also his friend and Ex-boyfriend Lorne Lyon, a rather timid and insecure Nemean lion that cannot help but to be upset with Jim's derparture. Emotional issues aside, Lorne, being a nemean lion, is very physically strong, capable of singlehandedly lift steel plates above his head, and has unbreakbly skin that can't be pierced by nothing but another nemean lion.