He'll go back to being adorable once he's through eating you.
Mr. Croup: You find us funny, Monsieur le Marquis, do you not? A source of amusement. Is that not so? With our pretty clothes, and our convoluted circumlocutions- Mr. Vandemar:(murmuring)I haven't got a circumlo... Mr. Croup: -and our little silliness of manner and behavior. And perhaps we are funny. [...] But you must never imagine, that just because something is funny, Monsieur le Marquis, it is not dangerous.
Matsuda Touta from Death Note. When Matsuda realizes that Light is actually Kira, he breaks emotionally and shoots Light's hand when he tries to use a piece of the Death Note. When Light tries again, Matsuda (who was once or twice hinted to be a decent marksman despite his silliness) flies into a furious Unstoppable Rage and then turns Light into swiss cheese with a barrage of bullets, only prevented from delivering the Coup de Grâce by the other officers.
Matsuda:"I'll kill him! I'LL KILL HIM! HE HAS TO DIE!"
Maximillion Pegasus from Yu-Gi-Oh! is more or less this trope. Most of his dialogue is that of mockery and he acts like a playful child. But underneath that is a cold, calculating villain who through ultra-powerful cards and mind reading can prove to be a dangerous opponent. And when you start beating him, he drops the goofiness and becomes dead serious. This attitude is best represented through his Toon Monsters: Very silly looking creatures, but with enormous power that is difficult to beat. When they are destroyed, Pegasus becomes much darker...
In Black Butler, we have Lau. You know, the goofy guy who constantly barges into the Phantomhive mansion and irritates the crud out of Ciel? it was all an act. Oh, and he was the head of the Chinese mafia.
Also Madame Red. The red-dressed, haired and eyed aunt of Ciel who sees him as her surrogate son? She's half of Jack the Ripper, punishing prostitutes for requesting abortions while she can't have kids because of an accident that also killed her husband; the other half being her seemingly-stupid but highly sociopathic shinigami butler Grell Sutcliff.
Grell still fits this trope when in his true shinigami form. Throughout the show, he spends a lot of time being essentiallyawalkingpunchline. It's very easy to forget that he's capable of killing people in cold blood, and that he's a strong enough fighter to hold out against Sebastian for several minutes (most people manage about two seconds).
The three bungling servants at the Phantomhive mansion. While they seemingly behave incompetently, the truth of the matter is Sebastian hired them as bodyguards to protect the mansion. Bard's a former soldier, Mey-Rin's an ex-professional assassin, and Finny has superhuman strength. The three managed to effectively force a gang of mobsters to retreat in their failed attempt to attack the mansion.
Well, they don't so much "force a gang of mobsters to retreat in their failed attempt to attack the mansion" as "brutally murder a group of seven highly trained assassins who were going in to kill them all." The most used sound effect in that chapter was Splat.
The Undertaker. He's a ridiculous Cloudcuckoolander who demands payment in jokes. He's also a highly trained shinigami, and as such can be extremely dangerous when he wants to be. Basically, Black Butler has an entire army of comic relief characters, and all of them are capable of doing very unpleasant things to you.
Mr. Percival Pompass, as he's called in the 1960's version of Astro Boy, seems a ninny comic relief from his whiny voice and habit of falling on his face; when action is needed, though, he's a tough fighter and a crack shot. Plus a reasonably good detective.
In Trinity Blood, we get a rare heroic example. Abel Nightroad is portrayed as a complete and utter moron throughout the entirety of the series. But beware! Threatening ANYone he cares about is a really bad idea. "Nanomachine Crusnik 02, output 40% approved." <<< This phrase activates an utterly terrifying demon monster that eats vampires. Moron, indeed BEWARE!
And just before the manga endedabruptly, female lead Esther meets a goofy, scatterbrained, lost-without-his-butler English gentleman namedCain.
One Piece lives and breathes this trope. Many a villain is introduced as an apparently harmlessweirdo who does things such as accidentally hypnotizing himself more than once, humorously disagreeing with the protagonist about the taste of a pie or just plain looking and/or talking funny. A few chapters later they turn out to be truly dangerous, usually without losing any of their silliness.
For that matter, some of the Straw Hats can qualify as this. The Captain Luffy may appear like a clueless idiot who only likes to eat meat but should youcrosshim, it won't be pleasant. Likewise with Cowardly Lion Usopp.
By the end of the Time Skip, the entire crew count as this. They might be one of the most eccentric pirate crews in the world-but they're also one of the most powerful and legendary ones as well.
Right, so, in Naruto, there's this group of bad guys. After one bites it, this minion of the Man-Eating Plant guy gets promoted to full miniboss-status. He seems kinda lame, but as it turns out, he's not only the organization's founder and secret leader, he's explicitly carrying out the Evil Plan of one of history's most powerful ninjas.
And now, he's become the Ten Tails' host. Remember, the last man who did that was the Sage of Six Paths, a man who could have killed Hashirama , The "God of Shinobi" with about as much effort and in as much time as it would have taked to look at him. He also created all ninjutsu and the Tailed Besats. By himself.
His partner Deidara was a candidate as well. Sure, his banter about art and his violent temper are funny, but he was able to take out Gaara and didn't do so bad against Sasuke either.
Speaking of Gaara, his demon Shukaku certainly qualifies. While he is amusing to watch and acts like a violent drunk, he is still very dangerous and was more than a match for the boss toad Gamabunta.
Might Guy as well. While the guy is a legitimate goofball, Itachi (the man who almost single-highhandedly wiped out one of Konoha's strongest clans) still considered him as a legitimate threat. In fact, he's one of the few characters capable of taking out a member of Akatsuki by himself.
Hell, a lot of the cast would fit this trope in some way. You've got Jiraiya, a hopeless pervert and Large Ham who is also so good at what he does that Pain has to hide half of his bodies just to defeat him. Guy's student, Rock Lee delivers Sasuke his first real beatdown of the series, kicks Madara so hard he splits in half and usually has to be a victim of The Worf Effect to be defeated. Even Naruto counts, being a notorious prankster and hyperactive idiot, as well as a serious heavy hitter. He gets his silliness from his mother, Kushina, who survived being Impaled with Extreme Prejudice an hour after giving birth to him and managed to restrain the Kyuubi with chakra chains just to protect her child.
Dragon Ball Z has the Ginyu Force, five goofy manchildren whose poses are Serious Business as they play rock-paper-scissors to decide who fights who and bet on candies on who wins. Their power levels and/or their physical and special abilities are no laughing matter. Guldo alone would have killed Krillin and Gohan had Vegeta not stepped in. The 3 together were absolutely no match for any one of the other four.
Also the last villain of the series, Majin Buu — a fat, childish, bubblegum-pink creature, which nevertheless was rightfully seen as the most dangerous entity in the universe.
Pokémon's Team Rocket would actually succeed in many of their schemes if the twerps didn't get involved. In Best Wishes, the silliness is completely dropped for Jessie and James, and at a minimum for Meowth.
Bleach: Mashiro Kuna is a former shinigami who is 100+ years old, looks to be somewhere in her 20s, and acts like an eight-year-old. Her appearances highlight her as a joke character who has tantrums in the middle of murder investigations because her partner won't pay attention to her protests that she's hungry. She fights by kicking things to death and occasionally fires off lasers with an area of 20+ yards.
Giselle Gewelle from the Vandenreich as well. She is a cheerful young woman who likes to make silly faces and snark at her friends. She's also a ruthless fighter who has no remorse when using her Blood Magic powers to force a bunch of soldiers to kill themselves.
Rurouni Kenshin has Kenshin, who is usually a polite, obvious moron ... and, if you push him too far, the legendary assassin Hitokiri Battousai.
The main character of Sasuga no Sarutobi is a perverted, meatball-shaped, troublemaker who jokes about everything. He's also near-invincible in battle.
Lord Death of Soul Eater. The goofy face, goofy voice, and general jokester personality can make you forget he's the guy who handed the Kishin his ass in a bag made of his own skin all those years ago. And be warned, Lord Death is by no means rusty.
Vash the Stampede from Trigun. He acts cowardly and stupid, providing general comic relief through out the show, but is in fact incredibly dangerous. If you piss him off (by hurting... pretty much any living thing) he can — and will — execute six precision quickdraw shots on your body, any one of which could cripple you. Why six, you ask? Because his revolver only has six chambers.
This often happens to be the case with characters from Fairy Tail. If a character looks or acts in a manner that seems strange, don't be surprised if turns out that they can kick 20 flavours of ass.
The Millenium Earl in D.Gray-Man looks like an obese grinning goblin with an umbrella that makes him fly like Marry Poppins and often ends his speech bubbles with a heart. Despite this, though, do remember that he's the God of Evil.
Pandora Hearts: Xerxes Break, the clownish servant of the Rainsworth family that constantly eats candy and carries around a doll on his shoulder. He was once The Red-Eyed Ghost, an infamous Illegal Contractor that murdered over a hundred people being pulled into the Abyss. He's also a Master Swordsman and has a contract with one of the most powerful Chains, the chain-killing Mad Hatter.
Also, Jack Vessalius counts, too. That sunshine demeanor and friendly attitude conceals a dangerous and insane underside. Same with Oz. Oz is also quite deadly when provoked. Try to insult Alice and he will cut you down with B-rabbit's scythe. Since he is also B-rabbit, that counts, too.
Sailor Moon, especially in the first anime. Usagi Tsukino is a ditzy schoolgirl who cries, whines and eats a lot. But she's also a powerful Magical Girl who will fight with teeth, nails and magic to protect those she cares for.
Enji Koma of Tokyo Ghoul is a prime example of not judging Ghouls based on their every-day personality and looks. Most of the time, he's a goofy Big Brother Mentor to the other staff at Anteiku, and brags about being a Retired Badass. He's generally dismissed by the younger employees, but proves he isn't all talk when CCG raids the cafe. Turns out, he used to be the leader of one of the most infamous gangs in Tokyo and spending his days serving coffee hasn't dulled his strength in the least bit.
His foe list has numerous villains who may be this way. For example, The Riddler mostly got into crime just to play mind games with Batman for fun. But from Commissioner Gordon's perspective, he's a Magnificent Bastard.
The Joker is portrayed this way in some cases, too. Once he paid for doughnuts with play money with his face on it. Play money impregnated with his special formula, which was absorbed through the clerk's skin.
Harley Quinn, though it varies more with her. Though mainly known for agility, people often forget that she also has superhuman strength (how else does she wield those giant mallets?) It's also easy to forget that she was a brilliant psychologist, and can revert to that personality to both apply those skills to mess with her opponent's head and to pass as normal far better than the Joker can. In her most recent incarnation, it's implied the Joker actually considers her more of a successor than a sidekick/girlfriend.
Granny Goodness is laughed at for being an old lady super-villain, until you remember that 1. She's the only minion of Darkseid who doesn't get her ass kicked on a regular basis by super-heroes/Orion and 2. She's the Goddess of Horrific Child Abuse on Apokolips, which means that whenever she is not scheming against Darkseid's enemies, she's routinely crossing the Moral Event Horizon with young girls and boys. Being a super-villain is certainly a hard job and despite her age, she is still around, so you know she's good. Also, being around Darkseid for any amount of time and not getting the Omega Beams or Omega Sanction speaks volumes as to how dangerous she truly is. Just imagine how bad her abuse has to be for it to qualify as "horrific" on Apokolips.
Ragdoll from Secret Six, no doubt. He's a master of the non sequitur, he's also perfectly capable of wrapping around you like a python and willing to snap your neck at the drop of a hat. In a recent issue, while attacking the rest of the team (and winning) he even gets a rant about people assuming he's just the comedy relief.
Mad Jim Jaspers from Marvel's Captain Britain comics - ran around an alternate universe England with a gang of ludicrous criminals, committing ludicrous crimes... and happened to be a Reality Warper of such magnitude that his entire universe had to be destroyed to prevent the Jaspers Warp from contaminating the multiverse at large. And his main universe equivalent is even more powerful... and a member of Parliament.
Zodon from PS238 is a Jerkass and the comic's bigtime Chew Toy, with most of his plans ending him up in greater trouble than he started. Problem is, this is usually because one of the teachers or the students got in his way — if they hadn't, the trouble — and much bigger amounts of it — would be someone else's.
Ambush Bug is a normal human in a ridiculous green suit amongst the gods of The DCU. In his heyday, he defeated a group of enemies with little to no effort while utterly humiliating them and could take on Superman or Supergirl before essentially defeating himself. Nowadays he's more relaxed.
Squirrel Girl looks and act doofy, has one of the silliest power in comics, yet defeated such omnipotent baddies as Doctor Doom and (seriously!) Galactus!
The Violator from Spawn. Taking the form of a pudgy clown, he's primarily around for comic relief. But at any time, the seemingly harmless clown can morph into a demonic killing machine, easily capable of kicking Spawn's ass.
Plastic Man is a zany, rubbery man who spouts silly jokes while having cartoonish adventures. He's also one of the most powerful members of the Justice League; even Batman, who has contingency plans to neutralise any of the League members in case they go rogue, is actively wary of him. On at least one occasion, he single-handedly took down a villain who had easily beaten Superman.
Foolkiller: In the limited series, Backhand, a local NY drug lord described Foolkiller as "crazier than The Punisher...He don't come off like no soldier or cop. More like being yelled at by your momma or a preacher". Admittedly, it is rather silly to lecture the person that you are about to kill. As they don't exactly live to benefit from the lesson imparted. Some of his kills occur after a brief debate in which he pokes holes in the other person's argument, then calls them a fool, hence the name.
Dr. Dinosaur from Atomic Robo. He may seem silly and incompetent, but out of all of the villains not only is he the one who survives, but he survives Jenkins. Nobody else has been able to do that yet.
Fables (being made up of fairy-tale characters) has a few examples.
On the villainous side, we have the Nome King who is initially an incompetent Blood Knightbrute to the Adversary. Upon getting power of his own he takes Stupid Evil to new levels, and his legal system is so ridiculous that a defence attorney brags about how brilliant he is at his job because he's managed to get a relatively humane form of execution for his client (who hasn't actually had a trial, even a show-trial), but his insane slaughter of innocents is not played for laughs.
Mister Dark has Talkative Loon tendencies so pronounced it's difficult to know whether he counts as Faux Affably Evil or genuinely Affably Evil, but since he is clearly introduced as a massive threat, they actually serve to make him creepier.
On the heroic side we have Bufkin the flying monkey, who generally acts as comic relief with his gullibility, heavy drinking and simian interest in his own faeces, but as a former captain of the flying monkeys and Fabletown's main librarian, he's a lot more dangerous than people realise when push comes to shove.
Transformers: More than Meets the Eye: Brainstorm is by all appearances a typical Mad Scientist, suggesting and designing weapons of unspeakably insane intentions. Then he goes and causes stars to go out. And then there's the fact that he's secretly a Decepticon agent, and all that wacky insanity is a coverer for a much darker personality.
Mukrezar is a whimsical, funny, likeable guy with a less-than-perfect record for succeeding in his many, many schemes. He is also one of the most cruel and sadistic Keepers.
This and OOC Is Serious Business are used horribly effectively in The Measure Of A Titan with Starfire. When she is upset enough to go out looking for criminals to brutally beat each night until she passes out from exhaustion, so much so that the crime rate drops as all the baddies try to stay under the radar, it cannot be a good thing.
Wolfang Richler does not seem like a very imposing villain at first, despite using his magic to blast off a statue's head. He babbles to himself, he seems to not believe people let themselves age, and his interactions with Jonahs paint the picture of a very lonely, immensely bored immortal. When Jonahs joins back up with his friends, we learn Wolfang turned two guards to stone, simply for getting in his way, and later in the same chapter seems to teleport all over the place, kills people with absurd ease and nonchalance, and during his conversation with Sarasho, we see he wants to set up a universe wide civil war.
In Kung Fu Panda, Tai Lung's attempt to kill Master Shifu was interrupted by Po. The snow leopard scoffs at the idea that this comical panda could possibly be the Dragon Warrior, only to find out the hard way that he most definitely is!
Disney's Willie the Giant from Fun and Fancy Free. In the first scenes of the Mickey and the Beanstalk segment of the film, Willie is introduced as a terrifying kleptomaniac who seems more storm cloud than giant. In his second entrance, he appears as a goofy shapeshifter with a fondness for pink bunnies, and an inability to pronounce the word "pistachio." Oh, and he's also a Big Eater who almost accidentally eats the Disney power trio of Mickey Mouse, Donald Duck and Goofy. But don't confuse his playfulness for dimwittedness like Mickey, Donald and Goofy tried to. Count yourself lucky if he keeps you as a literal souvenir in a box, rather than squishing you like an insect. And when Willie gets really riled up, he also wields an iron morning star the size of a two-story house.
Wreck-It Ralph's King Candy doesn't look all that intimidating at first glance. He's basically a CGI Expy of the Mad Hatter. But then comes The Reveal and by the time the movie ends, you will believe the Mad Hatter can be a legitimately dangerous villain.
The Lion King: Ed. Sure, he seems goofy and bumbling, with that laugh and blank wall-eyed stare, but Scar found out the hard way he can be deadly serious.
Flik from A Bug's Life is a light-hearted clown for most of the movie, but has a darker side which shows itself at the end when he tricks the Big Bad into getting himself killed.
Films — Live-Action
Tuco (The Ugly) of The Good, the Bad and the Ugly may be a Laughably Evil goon, but he is every bit as dangerous as Blondie (The Good) and Angel Eyes (The Bad), nearly killing them both on several occasions. Prior to the final shootout, Blondie makes sure to empty Tuco's gun rather than face him in a gunfight.
Yoon Tae-Goo (the Weird) of The Good, the Bad, the Weird qualifies. He provides most of the comic relief and is more prone to amusing mishaps than the Good and the Bad, but this does not mean he isn't capable of being incredibly dangerous. (Fittingly, he's an Expy of Tuco.)
In The Hobbit, with the exception of Thorin, all the dwarves in the company range from mildly goofy to downright mad at times. But they are all a force to be reckoned with when it comes down to a fight. Radagast the Brown is absent-minded and has bird poop in his hair but there is a reason why he is one of the most powerful wizards in Middle Earth, including banishing a herd of attack spiders from his home, brings a hedgehog back from the dead, leads a pack of wargs on a merry chase and manages to fend off the Witch King.
Mr. Croup in Neil Gaiman's Neverwhere even lampshades that just because something is silly doesn't mean it can't be dangerous. Then he and his associate Mr. Vandemar crucify the person who found them funny. While arguing whether circumlocution is a grammatical technique or a body part. (The former, if you were wondering.)
His second-in-command, General Melvar, almost goes to the opposite extreme. The persona he shows everyone but Zsinj is almost extraordinarily cruel, sadistic, and an Ax-Crazy idiot. When they're gone, his features are curiously bland, he enjoys startling his Warlord, and he's a Deadpan Snarker. They'll both kick puppies like there's no tomorrow, but they're more businesslike about it.
Nanny Ogg in Discworld is a prime example, looking like an amiably-wrinkled, sexual-innuendo-prone old woman, with a mind like a razor. She's been Granny Weatherwax's friend since they were girls.
Otto von Chriek from The Truth speaks in HEAVILY accented Vampire Vords, throws in a blah here and then (blah), is addicted to flash photography, which is bordering on a suicidal hobby for a vampire, and towards the end of the book clears a room of armed guards before ending it with a kiss to the forehead of their employer.
Lampshaded in a later book when someone realizes that Otto does this deliberately to blend in.
Little fussy Otto, in his red-lined black opera cloak with pockets for all his gear, his shiny black shoes, his carefully cut widow’s peak and, not least, his ridiculous accent that grew thicker or thinner depending on whom he was talking to, did not look like a threat. He looked funny, a joke, a music-hall vampire. It had never previously occurred to Vimes that, just possibly, the joke was on other people.
Pepe from Unseen Academicals seems like a goofy, Camp Gay fashion designer, but that's only when he's on the job. Off the clock, he's a hard-drinking, wise-cracking, street-smart fellow who's a veteran of the mean streets of Ankh-Morpork. What plants him firmly in this trope is a scene at the end of the book where Pepe corners street thug Andy Shank in a dark alley and carves out an eye as a warning to leave Trev Likely and his friends alone.
Albert Campion, protagonist of most of Margery Allingham's books. He might act like a silly ass, natter on about his mouse's birthday, and compulsively make jokes, but you should never underestimate his mental or physical capabilities. Ever.
Also, Alastair Barber from "Mystery Mile" who appears to be an embarrassingly-talkative bore who has a penchant for throwing food at acquaintances, is actually the Big Bad who runs a criminal network that is feared across continents.
Similarly, Lord Peter Wimsey plays the idiot man about town to the hilt, including carrying the requisite cane and monocle, and babbling on at the drop of a hat. The cane and monocle are secretly tools. Lord Peter is unstoppable as a detective. And it is seldom mentioned, but he is a war hero.
In Supernaturally, Jack seems to act like an immature teenager. He uses his Portal Door ability to appear in a girls' locker room and to appear in Evie's room to jump on her bed. However, he is secretly behind all the random paranormal encounters that Evie keeps having, because he wants to use her to get rid of the faeries. When she doesn't agree to do this, he banishes her into the Faerie Paths.
In Foundation and Empire, Magnifico Giganticus appears first as a rather pathetic clown before being revealed as a mutant telepath known as the Mule who conquers a significant portion of the galaxy and nearly destroys the titular Foundation forever.
Camp GayDandy Lord Akeldama in The Parasol Protectorate. He might dress outrageously and live in an overdecorated townhouse with a horde of Pretty Boy drones, but he's still a very old vampire. And those drones of his? He's trained them to be so effective at collecting gossip that he often knows more than the actual government.
Sixth Ranger and resident alien Ax is frequently played up as a comedic character, his infatuation with taste and tendency to play with sounds used for easy laughs. But when push comes to shove, Ax is the most dangerous of the Animorphs, beating out even Rachel. His feats include killing a rogue crocodile in The Reaction (after it beat half the team), defeating Visser Three in single combat as early as The Decision and even killing a Tyrannosaurus Rex in In the Time of Dinosaurs. This is highlighted pretty effectively in The Separation, when even Mean Rachel doesn't want to tangle with him.
And of course, Marco. The team's resident clown (if somewhat of a sad one), he spends half of his time making bad jokes and the other half viciously picking apart every plan of his friends and his enemies. In terms of planning he is the most ruthless Animorph—he does what he has to do, up to the point of once pushing his own mother off of a cliff. (She's the host body to Visser One. And they both survived, anyway.)
Oh, no. Hercule Poirot is investigating those murders I committed. But wait, he seems to be bumbling, he's very much the funny foreigner, and he's fallen for my Red Herrings. Maybe he's lost his touch with age. I think I'm safe. I—What the? How did he figure out... Damn! He got the goods on me for this murder and then tricked me into revealing what he hadn't known for sure.
In Lois Lowry's novel Number the Stars, Annemarie (at her mother's directions) acts like a "silly, empty-headed girl", convincing the Nazi soldiers that's what she is, instead of someone carrying a package vital to the Resistance.
The Doctor of Doctor Who just wants to have a bit of fun. "There's no point in being grown up if you can't be childish sometimes," he says. He's been accurately described as a "madman with a box", and no one with his dress sense (no matter how much it changes) could ever be taken seriously. He's also stopped more villainous plots and saved more lives than could possibly be counted, and is outright feared by some of the most evil beings in existence.
As befitting an Evil Counterpart, the Master sometimes shows shades of this. The Anthony Ainley and John Simm incarnations especially loved to bust out the Evil Laugh and add some flair to their villainy, but there is a very good reason the Doctor continually regards him as his worst enemy.
In the same way, River Song is a sweet, flighty, flirty woman...right up to the point where she reduces Daleks to gibbering terror by saying who she is.
Lothor of Power Rangers Ninja Storm. He spends most of the series sitting on his throne and cracking meta-jokes while his henchmen fight the Rangers for him, but is still a dangerous opponent whenever he can be bothered.
Rudy of Kickin' It is your standard Disnick Kid ComAdult ChildBig Brother Mentor, unless something really bad is about to happen at which point the writers remember what a third-degree black belt karate instructor's supposed to be capable of.
Jack O'Neill of Stargate SG-1 likes to play dumb and joke around, but gets things DONE.
Fran Fine, The Nanny, may come off as nasal, big-haired, and desperate, but, people tend to forget she is also a hypermanipulative master of the Cool and Unusual Punishment, most often in the form of forced proximity with her overbearing mother. She's also skilled with Jewish guilt, and can reduce feelings of triumph to bitter sadness with a snap of her fingers.
Rygel from Farscape is a deposed Hynerian (small, toad-like creatures) royal with an ego the size of a dwarf star and a tendency to either flee from battle or fart helium when pressed into a corner. He's also, at times, killed the man who spent years torturing him and paraded his head about on a stick, and tortured captive enemies to death for information.
Then there's "Coup by Clam," where Rygel has officially had enough of a blackmailing poisoner's shit, and thus bites his nose off, then poisons him in such a way that he can't possibly cure himself.
Walter Bishop from Fringe is a somewhat addled old man who constantly gets the name of his FBI overseer wrong, has an unquenchable taste for a different food each week, and often consumes drugs of his own making. In this context, it's somewhat hard to remember he was consigned to an asylum for years after a lab experiment that killed several of his assistants. And, when he's hooked up to the parts of his own brain, removed to destroy extremely sensitive knowledge, he shows how much of a righteous bastard he once was. He can also bring the fury in his current state - in "The Bishop Revival," he finds an ageless Nazi scientist has been using his father's research to design aerosolized poisons that target certain genetic markers. His response, in turn, is to design his own toxin, track the man down at a conference on peace and tolerance he'd been planning to target, and passionlessly cause him to asphyxiate in the middle of the gathering.
Alfie from House of Anubis may be the class clown, but he's no pushover, as he has proven to be a useful presence in Sibuna- and if he is serious about something, you better not stand in his way. He yelled at Fabian and Patricia when they wanted to have breakfast instead of rescuing the currently-trapped Amber, and then later was the one standing up against Sinner!Fabian- to the point of pressing Fabian's Berserk Button and getting away with it.
A case of Hoist by His Own Petard: Sometimes, Heels in ECW would throw out open challenges and the worst they would leave with was a bruised ego. After Justin Credible d. Chris Chetti at ECW Ultimate Jeopardy 97, November 8, 1997 (televised on the November 15th show), his manager Jason "The Sexiest Man on Earth" got on the mic and talked about how, out of 30 or so guys in the locker room, he was one of the few who could actually wrestle and that "it sucks" only working as a manager. So, since he was in his "street clothes," he issued an open challenge for a "street fight." Cue "Let Me Clear My Throat" by DJ Kool, and out comes...The Blue Meanie with Super Nova? Jason dismisses Meanie at first, but finally agrees. While it's not much of a match, and even less of a "street fight" (referee John Finnegan blocks Meanie from attacking when Jason ducks his head through the ropes), it qualifies as Jason basically treats Meanie as a joke the whole time...until Meanie comes up with a testicular claw into a schoolboy rollup for the pin! (For an example of how much worse this could have turned out for Jason, see Too Dumb To Live.)
Miss Piggy, full stop. She's a veritable empress among drama queens, insufferably vain, yet charmingly foppish, and is constantly comedically pining for the love of her employer, Kermit The Frog, who, half the time, doesn't notice her affections, and the other half is living in mortal fear of her affections. But, don't forget that a large part of her charm is that she's also a take-charge Action Girl who can become a Person of Mass Destruction at the drop of a (designer) hat. Plus, don't press her buttons if you want to live, i.e., don't insult her or her abilities, don't ever threaten her loved ones, and most importantly, don't make pork jokes in her presence. Well, you can if you want to, but, as The Muppet Movie demonstrated, she'll then open a six-pack of extra-strength whoopass on your minions, and violently install you in your own Mind Rape device with extreme prejudice.
Florian from Overlord II is a bumbling, useless buffoon whose entire purpose appears to be to embarrass the elven race, right up until it's revealed that he is actually the Big Bad and built The Empire purely so he could transform himself into a god. He also happens to be the one who triggered the magical disaster that turned everyone against magic in the first place.
Demyx from Kingdom Hearts II is a great example. The first time you run into him, on Hades' lair, he is running away from him. Then, during the battle at Hollow Bastion, you have to fight him. Pushover, right? No.
To an extent, Axel, for those who hadn't played Chain of Memories. At first, he's just a Punch Clock Villain who wants to grab Roxas and go home. Then you fight him as Roxas. Somehow, you never really forget that moment whenever you deal with Axel afterwards.
Dr. Eggman in Sonic Adventure 2 starts off the plot by personally destroying a big chunk of a top secret military installation and hacking the computer security system surrounding the Sealed Evil in a Can. And the first thing he did after getting the ARK and the Chaos Emeralds was blow up half the moon and give the entire world a 24 hour "surrender-or-die" demand. Eggman is over confident, but his track record kind of warrants it.
The aforementioned Sonic Unleashed opening shows what happens when anyone -Sonic included- underestimates Eggman, as it ended with him nullifying Super Sonic andbreaking the Earth in pieces.
The ending of Sonic Chronicles. Eggman doesn't go with the rest of the gang to stop Ix, claiming he needs to operate some groundside machine to let the others through. Thanks to the differential time flow inside Ix's prison, by the time Sonic et al get out, Eggman's rebuilt Eggmanland and may well have taken over the world.
And then there's Sonic Colors. Not only was he the Big Bad for the entirety of the game, but had it not been for a broken piece of a robot damaging a vital component of his latest weapon, he would've succeeded in his ultimate plan to mind-control the entire population of Earth with Sonic and Tails none the wiser.
Eggman had also managed to enslave three planets and an inhabited Asteroid Thicket, as well as build the largest space fleet seen yet, completely under Sonic's nose, and covered much of the land on all of the planets and asteroids with his own metal facilities. He would've completely snuffed Planet Wisp of life as well had Sonic not caught on in time, and he may have succeeded with Sweet Mountain.
Really, Colors would have ended up as a victory for Eggman if it weren't for one simple fact: The hero was actually being proactive rather than atypically reactive. Rather than wait for the villain to begin his rampage, the hero decided to investigate his machinations without any reason other than he is a irredeemable villain!
The comic relief character in any BioWare game usually doesn't appear harmless per se, but he/she/it is usually one of the scariest people on your team.
Neverwinter Nights was one of the first, bringing Deekin Scalesinger with its first expansion. A kobold bard whose songs are the wrong kind of good, and constantly makes some of the silliest, lampshade-laden observations possible. By the third expansion, he's also the best support character you can get, and also an epic-level adventurer who's got enough draconic blood to sprout wings and fiery breath, not to mention being the only one capable, without your intervention, of telling an archdevil to go screw himself when asked to betray you.
Knights of the Old Republic: HK-47 isn't the most effective combatant on your team, but he's an assassin droid tailor-built by the greatest Sith Lord in recent memory and has a very impressive kill count.
Jade Empire: The prime source of comic relief is BlackWhirlwind. He's half again as tall as anyone else on your team, he's got more chest hair than every other person in the game combined, and he dual-wields axes that look like the main character might have trouble lifting one.
Also, you can ask him about his past, and be regaled with cheerful and silly stories that prove beyond the shadow of a doubt that he's a terrifying sociopath who is capable of killing anyone for any reason, sees nothing wrong with this, and should not be allowed to be anywhere near innocent people.
Dragon Age II: Merrill's social unawareness and clumsiness form a major portion of the humor in the game. She's also a blood mage with no spells other than those designed to inflict very painful deaths.
Mass Effect trilogy: Jeff "Joker" Moreau is the snarktastic guy who flies the ship, and would snap in half if you picked him up and shook him hard. He's the guy who fired the shot that killed Sovereign. By the third game, he's considered the best pilot in the Systems Alliance, and possibly all of Council space. By a significant margin, at that.
The Volus in Mass Effect 3 multiplayer are 3-foot tall mole men with an obsession with cash, and while they can't exactly take on a 10-foot tall mech by beating it with its face like a krogan can, they have a lot of tech and biotic powers that manage to turn enemy troopers into so many red smears.
Now you can add the Batarian Gauntlet to their equipment. They can punch their enemies in the nuts so hard it causes their heads to explode. Explanation Killing an opponent with the Batarian Gauntlet Heavy melee causes their heads to splatter. However, this effect happens on every species, even when you're playing a volus, who are waist-high at most.
Bioware loves this trope so much that in Dragon Age II, the protagonist can be played with this personality. Snarky!Hawke frequently using Buffy Speak and Obfuscating Stupidity to lure their opponents into a false sense of security that they can't possibly be that dangerous, right? In reality, s/he frequently shows him/herself to be arguably the most intelligent of the three possible personalities.
During the Mark of the Assassin DLC, during their heist of Duke Prosper's vault, to distract a guard, Snarky!Hawke pretends to suffer an allergic reaction to a bee attack, falling to their knees as dramatic music plays;
Mega Man (Classic) has Dr. Wily who, like Robotnik, loses to a blue guy on a regular basis, but at the same time is a brilliant scientist capable of creating robots with great powers. His greatest creation, Zero, even outlasts Dr. Light's last creation, X, and saves all of humanity (though X was active for much longer).
Wily is dead and buried but his legacy has yet to fade from the series. The Virus he made with Zero was the origin of Sigma, and was adapted to make the Dark Elf.
Bowser is often portrayed comically and sometimes Mario will indeed be Go Karting with Bowser or challenging him to other games, but it's clear that he would probably succeed in taking over the world if Mario and Luigi and allies didn't keep thwarting him.
Mario himself. He's VERY happy-go-lucky, doesn't think twice about Go Karting with Bowser, and is sometimes a straight-up Cloudcuckoolander due to his overall lack of consistent traits. He's also incredibly strong and very nearly never loses a fight, even if his opponent has an unfair advantage.
Fawful in the Mario & Luigi series. Oh he may be funny with his similes and engrish and funny comments... but he manages to conquer the entire kingdom/world unresisted, mind controls pretty much the entire population and unleashes a monster that wants to destroy reality. He's especially this in Mario & Luigi: Bowser's Inside Story, where he gets promoted from The Dragon in the form of a villain's sidekick to the Big Bad and driver of the entire storyline.
This carried over to the Dissidia: Final Fantasy games. Yes, he's the Chaos Warrior most likely to crack a joke about farting, and has a walk silly enough to get him into the Ministry, but, when the situation calls for it, he's incredibly conniving and dangerous. In fact, it even turns out that he's the one who jumpstarted the rivalry between Cloud and Sephiroth!
And let's not leave out Gilgamesh, of Final Fantasy V. Every times he opens his mouth, it's for either a badass boast, a biting insult, or some random pop culture reference. Sometimes all at once. And, despite being both a complete nutter and the source of most of the game's funniest moments, he's still able to level entire armies singlehandedly, survive onslaughts from ancient sealed monsters, and oneshot an endgame boss. And this is before he started hopping The Multiverse.
Purge, from Space Channel 5 (part 2). At first, he seems just as goofy and camp as everyone else in the game. He constantly giggles, pelvic thrusts, and dons a sparkly purple disco suit for your penultimate dance-off. With Michael Jackson and a giant laser at your side, all it should take is one attack to finish him off! ... "Tch, yeahright!"
Dr. Mundo from League of Legends. He's huge, he's purple, he talks in the third person, he has a silly voice, and he has silly dialogue. He is also a serial killer who regularly engages in human experimentation.
Kaos, the Big Bad of Skylanders, is an Expy of Invader Zim. His first battle with the heroes ended with the Core of Light, the only thing keeping Skylands safe from the forces of Darkness, destroyed along with most of their HQ and all the Skylanders plus their Big Good MIA.
Ghirahim, the Big Bad of The Legend of Zelda: Skyward Sword, could be considered an inversion, as the "beware" side was seen first when he mentions that he created the tornado to capture Zelda. He displays his silliness in his campy lines and hand gestures after Link gets to meet him.
The Elder Scrolls V: Skyrim has Cicero, the mad jester and Keeper of the Night Mother. At first his wheezing giggle, eccentric personality and high-pitched voice are merely obnoxious. Then he attacks Astrid, wounds Veezara and disappears to the empty Dawnstar Sanctuary, after wounding Arnbjorn (a werewolf) in hot pursuit. He will continue to taunt the player from the shadows of the Sanctuary as the player fights through a legion of Spectral Assassins, though he grows increasingly panicky as the player continues to progress.
Sheogorath: Now you. You can call me Ann Marie. But only if you're partial to being flayed alive and having an angry immortal skip rope with your entrails.
Jasper Batt Jr. from No More Heroes 2: Desperate Struggle. Setting aside the fact that he used his pizza empire to climb to the top of the UAA and was the one who ordered the hit on Bishop, most players will think, "He's just a scrawny, bucked-tooth nerd with a hilariously bad sense of fashion. How bad can he be?" Then they actually fight the guy and he turns out to be one of the most irritating bosses in video game history.
Sho Minamimoto of The World Ends with You seems not such a big deal when he first appears. He's just some annoying reaper who screams in a megaphone and makes junk sculptures while talking in math. Even when you first fight him, he's not too bad. Oh, and he unleashed an army of nearly indestructible monsters on the UG and managed to come back to life in a new body that ends up being one of the hardest optional bosses in the game. Also, HE'S TRYING TO KILL GOD AND ALMOST DID IT TWICE.
Steven Heck of Alpha Protocol is a very silly individual: he rambles on about conspiracy theories involving the Federal Reserve having William McKinley assassinated and the government tinkering with the price of strawberries to control people's minds, gives Word Salad Titles to every covert operation that occurs in Taipei, is willing to use the Jack Bauer Interrogation Technique on someone to get him to remember where he put his car keys, and takes Time Cube quotes seriously. He is also, however, one of the most dangerous men alive, capable of wiping out entire rooms full of soldiers and elite intelligence operatives singlehanded. His method of dealing with the Chinese Secret Police agents who have Mike Thorton pinned down in the Taipei subway perfectly captures Heck's mix of silly and lethal:
"During the pursuit, Steven Heck (at Agent Thorton's request) arrived to offer emergency backup. Said backup came in the form of Heck crudely mounting a minigun to a subway car and firing wildly at Chinese secret police officers as his train passed the platform."
The final Team Fortress 2 "Meet the Team" video reveals something very disturbing about the Pyro: that he, she, or it (take your guess) doesn't see the world the same way everyone else does. The Pyro sees a rainbow blower, a bubbler; and lollipops, everyone else sees searing flames, explosive flares, and a mean fire axe. Pyro cheers for joy in a psychedelic dream world; others see Pyro cheer in sadistic glee, a burning town for a backdrop. In a way, it makes the Pyro even scarier.
The Spathi of Star Control are these ridiculous clam creatures who live in perpetual fear of virtually everything. They also advanced from the Bronze Age into the Atomic Age in under a century in response to the arrival of the Evil Ones, and a Spathi Eluder is one of the best ships in the game.
The Goof-off/Jester/Gadabout class of Dragon Quest III is just that - they will often disregard your commands and do something random and useless. Plus, they have all around low stats so they do very little even when they follow orders. Then they get a free class change into a Sage, which is one of the best classes in the game.
Veigar, from League of Legends, is generally seen as ridiculous in large part thanks to being short, having a very high pitched voice, and then there's the whole scheme to steal Bandle City's monument-thing using helium baloons and horseshoes. He also happens to have one of the highest burst damage potentials in the game, as well as being one of only two characters that has a potentially infinite offensive scaling.
The Tales Series loves to do this with its mole characters. There's usually one traitor per game, and while they mix it up enough to keep you guessing, it's often the biggest idiots who screw you over the hardest:
Tales of Vesperia has Raven, who acts like a grown-up and less flirtatiously successful version of Zelos. He, too, hands your female protagonist over to the Big Bad, and then reveals himself to be Captain Schwann, and then promptly kicks your ass so hard he's That One Boss for a lot of people. Like Zelos, the Big Bad makes the same mistake, and Raven returns to you later, despite the fact that the villain could literally kill him at any time.
Tales of Graces has a temporally inverted version of this. The bewaring comes first and the silly second. Young Richard is relatively quiet and melancholy, but then he gets possessed by the Big Bad Lambda and goes on the rampage. You spend most of the main plot bewaring of Richard and his terrifying winged form and his Voice of the Legion...and then he gets better, and Richard in the future arc is a Troll and a completely incomparable Large Ham goofball with his own line of fruit snacks.
Palutena, the Goddess of Light and the Big Good of the series is more of a Genki Girl than a goddess, a certified Deadpan Snarker who trolls Pit every opportunity she gets. But if the situation calls for it, she's just as capable of kicking ass. In chapter 3, if Pit takes too long to defeat Hewdraw, she'll summon the Sacred Goddess Clobberlaser to oneshot it. She also serves as the boss of Chapter 20, showing just how powerful she can be when she decides to cut loose.
Hades is essentially this game's Tim Curry. His flamboyant, snarky and sometimes flirtatious attitude makes it hard to take him seriously. But this is the God of the Underworld and is as every bit as powerful as a Physical God should be as his fights with Pit will attest. This is a guy who can and sometimes will destroy entire countries for fun and is cunning enough to get entire nations to fight each other over a nonexistent item.
Thanatos, the God of Death is basically an Expy of The Mad Hatter. He's childish, goofy, and a bigger Butt Monkey than Pit himself. But he is likewise far from harmless. This is especially in the anime short Thanatos Rising where he effortlessly defeats a human army and takes control of their Trojan horse tanks. And he nearly kills Pit soon after.
Viridi, the Goddess Of Nature, is one of the snarkiest characters in the game and looks (and acts), like and eight-year-old brat. But as her debut chapter shows, her capacity for destruction is deadly real thanks to her Reset Bombs.
Pyrrhon, the self-proclaimed Sun God, is the biggest Ham in the game and the epitome of the over-the-top superhero parody. His loud, boisterous attitude makes it hard for anyone to take him seriously... At least until it's revealed that he was using everyone's help to take control of the Aurum Brain and become the strongest god in existence. But then his plan backfires a few minutes later.
It'd be hard to list all the Touhou characters who don't qualify as this, due to their wacky plots and hijinks, and the dangerous (or potentially-dangerous) powers they're capable of using.
There are quite a few comic-relief characters in the Ace Attorney series, several of which have committed crimes.
Luke Atmey takes the cake. It's rather difficult to take this particular blowhard seriously, until you learn he was the mastermind between several thefts thought impossible. In fact, while Atmey is a PridefulAttention Whore, he also qualifies as an Insufferable Genius and even a Magnificent Bastard, getting you to have him accused of theft just so he could use that as an alibi for a murder that happened at the same time—a murder he actually had committed!
Dawn of War II: Retribution: While Warhammer 40K orks are plenty silly in general while also being plenty deadly, the ones followed in the Ork campaign take both these traits further than usual. The silly? They treat a gigantic war machine like one'd treat a puppy (complete with walks), have a stealth specialist that once tried to hide in lava, and their leader is a space pirate, complete with hat and attire, among many moments of gleeful lampshading and general black humor. The dangerous? This band of lunatics easily stomps several recently-defected chaos bases, take down the Eldar campaign's own hero, finish off an entire craftworld, manage to track down a Space Marine chaptermaster through logic alone (where even the Eldar failed at first, mind you), beat the living hell out of him when he had ascended to greater Daemon only minutes ago, and blow his head off with a captured asteroid, and, to top off these and many other acts of wanton looting and burning, depending on the optional missions taken, they simply leave on their new ship, looking for more planets to loot. The new ship being a gigantic dreadnought that had been stuck in the Warp for so long it was basically the Event Horizon's bigger brother. Oh, and their leader also mugged Inquisitor Adrastia for her Nice Hat.
Black Mage is The Chew Toy of 8-Bit Theater and spends most of his time stabbing Fighter and failing to get into White Mage's pants. A few times, however, he's acquired enough power that he decides he doesn't need his companions. On these occasions, he shows in no uncertain terms that he's not joking about being an Omnicidal Maniac, and he has come very close to wiping out reality. On one occasion, he finally succeeded in murdering the rest of the Light Warriors only for Sarda to resurrect them just to screw with Black Mage.
The Jaegermonsters known as da Boyz in Girl Genius are variously-hued, apparently dim (except for Dimo, who is often the Only Sane Man of the trio) Funetik Aksent speaking comic relief...until it's time to fight, and then readers are reminded that they are brightly-colored engineered super soldiers who do not just have pointy teeth and sharp nails for decoration.
Hell, just Jaegers in general. They all have that accent, all of them like their hats big and shiny, and all of them would joyfully run into a huge, bloody battlefield like a kid would into an amusement park, before tearing up entire squadrons barehanded. Even their generals, who are several centuries old, have no qualms joking around in a skirmish, to the point four of them decided to have a little body-count competition, with one of them spending most of the battle getting the rules straightened out, during an invasion on their hometown. And they stomped the everloving hell out of the invaders, with the general that wasted most of the battle winning the competition by way of blowing up the airship carrying the entire force.
The Courtyard Droll counts too. Despite working for the evil Dersites, he's a Cloudcuckoolander whose version of torture involves swapping hats with someone - and a terrifyingly effective assassin with a bodycount that includes both Jade and Jake's dreamself. For comparison, Hegemonic Brute, The Big Guy of the agents, managed to accumulate zero kills before his death in both universes.
John, Jade and Nepeta also count. With the exception of Gamzee, they are the silliest of the heroes. Nepeta is able to kill large wild animals with her bare hands, John, upon becoming a wind god, creates a massive tornado which he uses to drill to the centre of a planet to retrieve a massive bomb, In Cascade, he creates lava tornadoes and defeats the largest enemy seen in the game with a single hit, and sometime later becomes the first person to land a hit on Bec Noir, dealing about 1/10th of his health in damage off of one hit. When Jade reaches God Tier, she becomes fused with Bec, making her probably the strongest member of the group.
Head Alien of It's Walky! fame generally comes off as a cartoon villain, constantly dreaming up plans doomed to be easily foiled by the introduction of the heroes, who never passes up the opportunity to show his love for dramatic tension, even when doing so hinders or even cripples his plans. He always managing to further some goal every time he is effortlessly crushed, and all it takes is a moment of talking before he's got you trapped with a Breaking Speech, eating out of his hand doing exactly what he wants.
The title character himself counts, considering he spends much of the series as a Man Child. Even if it's partly an act.
Xykon spends much of his time as borderline comic relief: much of his villainy appears to be of the card carrying variety, and many of his interactions with his supposed subordinate Redcloak imply that the latter is the far more intelligent of the two. This all obscures the fact that Xykon scares the pants off of Redcloak; even though he's the high priest of an evil god, Redcloak's goal is equality for goblins, orcs, and other races that are normally just cannon fodder, while Xykon's goal is more or less "Take Over the World and inflict as much pain and mayhem as undeadly possible".
Even with the heroes out to stop him, he's a credible threat to the entire world. They kind of beat him the first time kind of by accident, but since then they've been lucky to get away with their lives when tackling him (and not always so lucky), and that's with him conquering a city and beating its forces at the same time. (With Redcloak's help.)
The time when he took on the entire roomful of Sapphire Guard makes this even more apparent. He starts out by tossing a super bouncy ball at them, which was inscribed with a Symbol of Insanity that made them kill each other. Xykon got a whole lot less funny all of a sudden. He even commented that he could've just kept to the air and blast all of them. The only reason he had the Sapphire Guard kill each other was because he thought it would be "going the extra mile".
Xykon's Batman Gambit in Start of Darkness: Xykon tempted Redcloak into killing his brother Right-Eye to protect him. The Breaking Speech that follows speaks for itself.
Xykon:So therefore, you're just going to continue following me and doing whatever I order you to do. Because as long as you're loyal to me, I'll let you pretend this never happened. We'll just go about our daily business, and you can hide from the horrifying truth of what you've become - namely, a murderer who just killed his baby brother in cold blood. And hey, we can pretend that you don't really have any options about any of the despicable actions I ask you to take here on out rather than acknowledging that, like Right-Eye, you do in fact have a choice. But unlike Right-Eye there, you're too chickenshit to ever make it. You'll obey me forever now, because I give you an excuse for your inexcusable behavior. Now, are you going to stand there and tell me I'm wrong? Didn't think so.
In the Linear Guild, Thog the half-orc. Because he's a funny, ditzy, childlike blithe spirit, people (readers especially) tend to forget that he's a killing machine prone to Unstoppable Rages when he gets bored (like, say, if he runs out of ice cream).
The Monster in the Dark is this in two directions simultaneously. Firstly, it was introduced as a terrible monstrosity only to turn out to be somewhat dim-witted and quite possibly harmless. Secondly, after spending a long time behaving in a very child-like and friendly manner and doing nothing else, we got a few clues that the Mit D might in fact be an exceptionally powerful (and thus potentially dangerous) creature. Its true nature has yet to be revealed.
Lewie the Lich of Yet Another Fantasy Gamer Comic is initially kind of laughable. Then he decides to try playing Sauron, and after a couple of misfires (beholders can't wear rings...), he enslaves a mountain of monsters.
This trope could actually be considered the hat of many of the comic's protagonists, both monstrous and otherwise. Just for another example, here's what can happen if you underestimate one of the bigger Cloudcuckoolanders on the mountain...
Coyote in Gunnerkrigg Court has incredible power at his command. Most of the time, he just uses it to have fun without causing (too much) trouble. On occasion, however, he uses it for very cruel acts.
Cucumber Quest: YA BOY NOISEMASTER, the second of the Disaster Masters to show up. While smarter than the first he's a colorful hammy DJ who's Jive Turkey demeanor hides a cunning mind. His "hype man" personality is later revealed to be an act used to annoy his boss, and underneath that he resents the Nightmare Knight and tries to defy his role in the story by blowing up an entire city.
One could argue that wasn't exactly a reward for good behavior.
Also, according to some interpretations of the Continuity Snarl, that one was a clone.
The Noisy Tenant series of Creepypasta is an entire mythology of this. It's an entire building complex of whimsical, decrepit recreations/mockeries of modern places, like Silent Hill designed by the same people who did Pee-Wee's Playhouse. And it's filled with funny and whimsical inhabitants like Dr.Phage, a smiling man-sized bactereophage with a ridiculous bow-tie who performs horrible and unnecessary surgeries on people who end up in his office. Or Harmburger, a tottering anthropomorphic hamburger who tries to slaughter people in his freezer of alien meats or, with the help of similarly whimsical/horrible chronies resembling an anthropomorphised barbecue grill and meat grinder, brainwashes all of humanity with his tainted meat, which also infects them with horrible parasitoid brain-flies that are then sold to some other dimension, in the burgrr.com ARG/creepypasta.
The Evil League of Evil in Doctor Horrible's Sing-Along Blog features such silly gimmicks as Dead Bowie and Fake Thomas Jefferson, but they're all unrepentant murderers at the very least.
It says something that the League's leader is a horse that seems to be universally recognized as the embodiment of all evil.
The Evil Mastermind, an Evil Genius from the Global Guardians PBEM Universe, is this. He favors grandiose schemes within schemes within schemes within schemes. (Whaddaya want? He's a super-intelligent twelve year old boy.) Most of the heroes consider him a joke. But you know, he did almost poison New York City's whole water supply that one time. And other time he actually had control of the nation's air traffic control systems for nearly half an hour...
Generator (Jade Sinclair) of the Whateley Universe. She's cute, she's wacky, she invents crazy stuff, she looks like she's only ten... She stopped a supervillain with the powers of the werewolf by nailing him to a tree with railroad spikes. She destroyed a Syndicate hardsite by killing their minions and making it look like she had turned them into zombies. Her shoulder angels nearly caused warfare across the Whateley Academy campus.
Ron could also fit: when he is temporarily made a villain in one episode, he's unstoppable. Shego (who rightly shows disdain for her boss Drakken's incompetence and demonstrated in the first movie how incredibly dangerous she'd be if she treated villainy as more than just a job and applied herself) is terrified of Evil!Ron.
Lucre was also a surprisingly effective villain with his lame gimmicks.
Dr. Robotnik as he appeared in Adventures of Sonic the Hedgehog is regarded as less competent than his deadly serious Sonic Sat AM counterpart. But he and his robot minions Scratch and Grounder execute any number of formidably dangerous plans to take over Mobius that only fail because of Sonic, and they often succeed at capturing or otherwise incapacitating Sonic. It often happens that Sonic's actions do nothing more than undo the damage that Robotnik had already done.
The supervillains in The Venture Bros. are indulged for precisely this reason. In particular, the Monarch seemed content for years to engage in a cat-and-mouse (or "cat-and-also-cat" as he described it) rivalry with Dr. Venture, preferring to live out a hero/villain fantasy with the disinterested scientist than actually kill him when he had the opportunity. The early episodes would even make him seem like a Harmless Villain if not for his habit of killing his own henchmen. Then he loses the right to arch Venture, and promptly murders his next five archenemies out of frustration.
Cheryl and Pam of Archer are for the most part a cheerful head case and a horny, fun-loving Gasshole respectively, but Cheryl is also a pyromaniac who once threatened to crash a helicopter she was a passenger on just to drag a confession out of her brother, and Pam is a full-blown Bad Ass who paid for college by fighting in underground combat leagues— killing more than a couple of opponents in the process.
Skeletor from Filmation's He-Man and the Masters of the Universe (1983) was portrayed in a ridiculous manner at times, but there's no doubt that if He-Man and his allies didn't exist, he would have been able to create much chaos and, possibly, take over Eternia completely.
Self-proclaimed boy genius Jack Spicer from Xiaolin Showdown starts off as the main villain but slowly slips into a mockable state as more powerful villains show up, even to the point of being a fanboy of the Prince Of Darkness, Chase. By season three, the Xiaolin monks are defeating him for sport, fight scenes with him last on average three minutes, and he only lays claim to one Shen-Gong-Wu, the ridiculous Monkey Staff. Cue the season finale, Time After Time pt. 1, where Omi freezes himself to get to the future, and in his absence, Jack takes over the world, including imprisoning the remaining three Xiaolin warriors and the three main villains of the show.
In spite of the silliness of the show, the villains from Freakazoid! managed to be more or less serious enough to appear dangerous. But if you look at him from the perspective of the bad guys, Freakazoid himself completely nails this Trope.
In The Secret Show, a villain simply known as 'The Clown' appears and babbles on about taking over the world, while seeming completely ridiculous. The main characters decide to ignore him in favor of more visible threats, and The Clown, unopposed, takes over the world in short order.
Most of the time, the title character of Invader Zim either falls victim to his own Genius Ditz nature or completely fails to properly use his extremely advanced technology. The few times he's half-way competent however show that he is very good at causing large scale mayhem and destruction, even if sometimes he destroys the wrong thing.
In one episode, Zim locks GIR into "Duty Mode" (the red-eyed, serious version), and he promptly becomes much more evil and competent than Zim himself, including deciding that Zim is a threat to the mission and needs to be eliminated. Long story short, Zim just barely turns him back to normal in time to prevent a Klingon Promotion.
Unlimited episode "Flash and Substance" focused on the Flash and his Rogues Gallery. Flash's villains might be incredibly silly theme-based, pun-spouting Punch Clock Villain holdovers from the Silver Age, but when the fighting breaks out they're able to easily take out Orion and fight competently against the Goddamn Batman.
Flash himself is an excellent example. Wise-cracking hero with a friendly and cheerful disposition, constantly flirting and a hopeless romantic... who is also one of the most conscientious of the League in regards to collateral damage, regularly talks villains into giving up, and, if that doesn't work, can single handedly defeat living gods like Brainiac merged with Luthor.
Transformers Animated: Prometheus Black/Meltdown, despite his Disco Dan style outfits and cartoony Mad Scientist nature is, by far, the most dangerous human villain on the show. That may not seem like much, considering the other villains, but he's almost on the same level of evil as the Decepticons. While other human villains at most got a single episode of being at all dangerous, Meltdown was consistently portrayed as a genuine threat nearing if not equaling the Decepticons — who in this continuity, are incredibly dangerous threats that are more than a match for the team on an equal playing field.
Among the Decepticons themselves, there's several cases of this.
Blitzwing, with his Split Personality and his wacky Random face is such a riot that sometimes you forget he's a merciless giant war machine who's armed to the teeth and capable of hunting you down by land or by air.
Swindle is an Arms Dealer with mannerisms based on Ron Popeil.
Despite his overinflated ego and propensity for running his mouth, Starscream can be surprisingly cunning and dangerous.
One episode of Aladdin: The Series had the recurring villain, Mirage, convince Chaos, who was visiting, to make a little, well, chaos, in the palace of Agrabah where Aladdin and Jasmine are holding a dinner for some nobles. Chaos is a silly blue cat with wings. He also has more power in his whisker than a palace full of genies, can grant his own wishes, shrunk Jasmine to the size of an insect and nearly got her stepped on by her own husband when she ordered him to stop his mischief, and was able to poof up an Evil Twin that Aladdin was forced to fight to a near standstill after Genie mentioned the only predictable part of Aladdin's adventures was he always won. Chaos terrifies Mirage, who is the current personification of evil, and who has proven quite capable of offing the heroes and wiping Agrabah off the map. And after the series, Chaos appeared one last time in a short Aladdin comic in Disney Adventures Magazine in a Deus ex Machina type ending by stripping the powers of a devilish entity known simply as "Evil", who was near to defeating Aladdin, when he felt things were getting too predictable.
The Duke of Detroit from Motorcity. Dresses like a really rich guy out jogging, is Large Ham personified, and loves to break out into random karaoke. He's also one of the most influential people in Motorcity, with enough wealth and artillery at his disposal to make your life a living hell, anytime he sees fit.
Old Man Mcgucket, the local kook, has proven himself perfectly capable of mass destruction. In "Legend of the Gobblewonker" we learn he builds highly-destructive Humongous Mecha as a coping mechanism for rejection and loneliness, and in "Land Before Swine" it's implied he ate his way out of the belly of a pterodactyl.
And then there's Bill Cipher from "Dreamscaperers", an Eldritch Abomination whose goofy appearance and laid-back personality hides massive amounts of power.
And that's completely ignoring Stan Pines, who goes through great lengths to make as much money from each and every situation he finds himself in. Stuff his great nephew in a wolf-boy costume and make him dance for money? Get into a wheel-of-fortune-esque television show through pure greed and selfishness, only to tragically lose because he literally didn't know what the word "please" was? Par for the course. But if you threaten Dipper's or Mable's lives, he's quick to beat the shit out of you and anyone you may have helping you. As a horde of bloodthirsty zombies could attest, if they were currently dead. Again.
Varrick from The Legend of Korra may act flighty and absentminded, but he hides behind that ditzy exterior a ruthless Corrupt Corporate Executive who is willing to start a civil war between the Southern and Northern Water Tribes just to grab a few bucks from the conflict.
Ty Lee from Avatar: The Last Airbender is a bubbly, cheerful acrobat who babbles about reading people's auras and does things like walking on her hands for no particular reason, but when she actually fights, she is more terrifying than an army of Firebenders.
Also Avatar Aang, the only person scarier than Ty Lee. He is generally a bit "air-headed", enjoying penguin rides, fruit pies, and bad jokes, not to mention that he is a Technical Pacifist. But there's a reason it's Technical Pacifist: provoke him, and he can and will Mind Rape you and rip out your soul.
King Bumi appears to be a crazy old man who loves candy, bad jokes and ridiculous outfits. However, he's also one of the strongest Earthbenders in the world, and took back an entire city from the Fire Nation in under eight minutes (Granted, the Fire Nation soldiers were depowered due to an eclipse, but that doesn't stop Bumi from crushing tanks like beer cans and throwing buildings across canyons).
The teddy-bear cholla, a cactus native to the deserts of the American southwest, from a distance looks as cute and fuzzy as the name implies. Those fuzzy-looking spines, however, frickin' mean business! Entire segments of the plant will break away and cling to their victim like a gigantic, vampiric cockleburr. This is also simultaneously the teddy-bear cholla's main defense against herbivores and their primary form of reproduction (in that the segments sprout as soon as they're removed from their victim). They tend to grow in patches, making large swaths of the Sonoran Desert impassable. The cactus is so devious that locals like to repeat an old wives' tale that claims plants are able to reach out and stick passers-by, which, by the way, inspires its other common name of "jumping cholla."
The platypus is an odd animal, even among the grab-bag of evolutionary oddities that make up the ecology of Australia. Possessing a duck's bill, a beaver tail, and ottter-like feet, it further distinguishes itself by being one of only five species of mammals to lay eggs. Beware the male ones, though, as they produce a venom that causes excruciating, intractable pain in humans, lasts for weeks and is noted for not responding to analgesics like morphine. This venom is not actually fatal - but a dose of morphine that is will not make a dent in it.
Guess which animal in Africa has killed the most people? Black mamba? Lion? Cheetah? Hyena? Human-baby-eating-monkeys? No, my friend. It is the hippo. Yep. The big fatty with cute little ears. Word of advice: When in Africa, don't ever go near where a hippo lives, because they are territorial and if they see you, they will chase you and you better have a runaway truck nearby, because they are faster than they look. Why should you be so worried about escaping an angry hippo? Why is the death rate so high? Hippos aren't afraid to bite.◊
Caterpillars are a perennial source of visual amusement for humans. After all, the typical caterpillar is soft, fuzzy and too interested in eating to notice the big humans poking and gawking at it. However, there are some caterpillars that, despite looking rather peculiar or ridiculous, are actually dangerous. One offender is the caterpillar of the puss moth, which is a big, fat, green caterpillar. If threatened, it rears up to show off its big, pink head, which it sinks into its neck, so that one sees a face with what appears to be a pair of lips underneath its mouth. Any predator (animal or human) that does not get the hint to leave it alone from this threat display will then find out that the "lips" serve as the opening to a gland that squirts out a jet of caustic formic acid. The caterpillar of the flannel moth is far worse, appearing as a disheveled and strangely adorable ball of fluff. Do not touch any caterpillar with the nickname "asp!" The fluff hides numerous venomous spines that cause excruciating pain, comparable in agony to snakebite, and, with the added bonus of causing bleeding, blistering rash at the site of contact.
Rhubarb looks alot like Celery with a red or pink stalk (it can have a green stalk too, so beware). The leafstalks of both plants are edible, as are Celery leaves. Rhubarb leaves, however, have so much oxalic acid concentrated into the tissue so as to be deadly. While oxalic acid is what gives rhubarb its deliciously tart flavor, in large quantities, it can cause immense harm, in that, at toxic doses, crystals of oxalic acid will form in the blood, and when the blood is filtered through the glomeri of the kidneys, these crystals will lacerate the tissues of the kidney, so that the poisoned person will bleed to death by urinating blood.
The Cape Buffalo: It looks kinda like a big dumb cow, but beware, this massive bovine is considered one of the Big Five of African big game (Said list contains lions, leopards, rhinos, and elephants. That's right, this (allegedly!) big dumb cow is considered to be on the same difficulty level as lions and elephants), and is known as the Black Death to professional game hunters, due to how hard they are to kill, and their tendency to hunt their hunters back if they've been wounded. They are known to ambush game hunters (and lion cubs) and kill them horribly by goring and trampling them to death. They're herbivores, but kill more humans, per year, than lions do.