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 mangrit, 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.
Deconstructed by Tavros, who is... not so much "moron" as "naiive, clumsy, and completely lacking in initiative due to years of Mind Control and emotional abuse", but it still prevents him from effectively using his Game Breaker abilities, and ultimately leads to his demise. Reconstructed later on, though, when he manages to lift his chains.
Jake may be a bit slow on the uptake, and kind of a crybaby, but don't mess with him — his Hope powers are among the most powerful in the game.
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 agreed: 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".
Thog is probably the most blatant example of this. On one hand, he's a complete idiot who rivals Elan for the lowest Intelligence score in the comic; on the other hand, he has the strength to toss people around like beanbags, and is mentioned to have solo-killed a stone giant with PC class levels at one point.
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 badass 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 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.
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.
Unity from Skin Horse is an interestingly inverted example. She's a sociopathic, nigh-unkillable undead murder-machine created by Mad Science all the time, but when she's eaten a sufficient amount of braaaaaains (or just one really GOOD brain, even if it's cybernetic), she turns into a supergenius capable of out-thinking everyone from the Omniscient Council of Vagueness on down, often dissecting their Gambit Roulette in front of them. So basically, a crouching moron, INTELLECTUAL badass. Her team-mates even pointed out how, considering that she still has her superhuman strength in this state, she's a lot like one of those runs of The Incredible Hulk where he gets to keep Dr. Banner's intellect even while hulked out. Other than the 'brainy' aspect, she's otherwise a straight example, right down to forgetting everything once the braaaains wear off. (She's occasionally resorted to writing notes to herself... with mixed results, since her normal persona is as likely to turn a note into an origami dinosaur or a quick snack as to read it.)
There's also Tip, a weaker but more traditional example. Being a Wholesome Crossdresser, psychologist, diplomat, and part-time Pornomancer, he's generally the one who has to do the boring stuff like actually try to TALK to their clients. Or... pumping people for information. Regardless of gender and species. But when things have gone thoroughly pear-shaped, it quickly turns out that he's actually a full-blown Agent Peacock - with a decorated military background and a compact, yet powerful Hand Cannon concealed somewhere on his person at all times. Apparently he's gone through Afghanistan and earned his rank rescuing 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 one single strike.
Donald: WHY DID YOU EAT SANTA YOU BIG BLUE MEAN FFFUCK?!
Nyte: Is it a good thing or a bad thing this will only work once a year?
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.
Mr. Fish's trainer, Jared Kowalski, qualifies as one in his own right. He's extremely childish, interacting best with Commander Badass' small children, utterly irresponsible, has the attention span of a chipmunk on meth and fails to understand basic concepts. Like Pokeballs. He is also an extremely competent trainer, not only managing to raise and tame the largest Gyarados Lysandre had ever seen without a pokeball, but also captured several dozen Magnemites to build Mr. Fish a suit of armor, after someone mocked the Gyarados' weakness to electricity. On top of this, Jared has proven himself as an indispensible PA to the Commander, and his actions during the Nomura Syndrome plague earned him the respect of all the manly guys. In an alternate timeline where the Commander vanished, Jared took his place, edging out Kratos as the leader of the Manly Guys.
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 "Borogove" (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.
At first glance, Nessie from White Dark Life is a ditzy, if smart, mermaid. You'd still expect her to be useless in in a fight outside confusing people right? Well you'd be right if she didn't have a penchant for weaponcrafting.
The main character of YOSH, Phil, used to be your average dopey romantic-comedy type protagonist. Loyal to his friends, unprejudiced and open-hearted, possessing nothing even resembling a temper... or a clue. Then the comic took a right on the corner of Drama and Cerebus, and his proven ability to survive comedic injuries was revealed to be the result of him being some kind of destined, indestructible Anti-Magic superhero, thrusting him into the center of events that will determine the fate of the world. His personality has barely shifted, but by now, he's happy to walk up in front of killer robots and demonic undead creatures that can threaten master-class Ninja and Powered Armor Mercenaries, calmly declaring "They can't even touch me", and kicking epic ass. Usually leaving anyone who wasn't aware of his powers and the training he's received by now gaping in surprise.
Heck, even before he received the training and gear needed to actually USE his powers offensively, he frequently proved a game-changer, supporting his more combat-capable friends... as a human shield/bait/blunt weapon/improvised projectile combo.
Sgt. Schlock of Schlock Mercenary is a goofy Man ChildBlood KnightComedic Sociopath, and is generally a source of the webcomic's humor. However, when the going gets tough, Schlock becomes an effective soldier and has shown keen insight and foresight.. This exchange is what the rest of Tagon's Toughs think of him;
Murtaugh: I don't understand him. Sometimes he seems to function like I expect a grizzled sergeant to. You know, correctly.
Dr. Bunnigus: And sometimes he functions more like an overstimulated child? Yes, it takes some getting used to.
This applies to about half the Toughs, though more the thinkers being surprisingly tough than the grunts being surprisingly smart.
One-Punch Man is heavily built around this trope. Saitama should by all rights be The Dreaded, but between his silly costume, his bald head and his carefree demeanor, neither heroes nor villains can ever seem to take him seriously. Hell, his hero codename is "Caped Baldy"! Much of his behavior is due to him being jaded from being too strong for anything to be a challenge anymore.
Dr. Phage in Awful Hospital is a ditzy Mega Microbe with a colossal ego, an infinite collection of bow ties, and highly dubious medical qualifications. He's also a front-line care provider for anything in the Multiverse that gets sick enough to end up in The Hospital, shows exceptional competence when he's dealing with life-forms he's more familiar with, and makes "messy work" of intruders on his turf.
Lalli from Stand Still, Stay Silent is such a Cloudcuckoolander that he is often left not understanding what is going on and has No Social Skills. However, when given a direct order and/or the situation is very obviously "Plague Zombie monsters are attacking", he can get extremely focused on his task and shows great talent in both battle and magery. His mage senses also make him more aware of incoming threats than others. The difference has caused Emil to have a Big Brother Instinct towards him despite actually being the New Meat of the crew while Lalli is a grown up Child Soldier.
Onni is... well, lazy is the wrong word, but rather content to not have to leave Keuruu, and actively resists having anything to do with the Silent World. However, get him going and he can Total Party Kill a horde of Plague Zombie Monsters from a couple of countries over without so much as breaking a sweat.