He'll go back to being adorable once he's through eating you.
Mr. Croup: You find us funny, Messier 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, Messier Marquis, it is not dangerous.
Pictured above is Gluttony from Fullmetal Alchemist. Of all of the homunculi, he's the only one who's played for laughs, since he's fat, dumb, and overall acts like a lovable dope. There's also the fact that he's very innocent, and only does what he does because his higher-ups tell him to, and he genuinely doesn't see any wrong in what he's doing. However, as his name suggests, he has a bit of a hunger streak. In the manga and Brotherhood, it's not helped when he's reminded of Lust's death by Roy Mustang's hands, which drives him into the monstrous state also shown above.
Etemon in Digimon Adventure. Yes, he's a wannabe rock star comedy monkey, but that never stopped him from curbstomping the protagonists every time they saw him. The fact that he's a level higher than them and can negate their ability to powerup helps tremendously. He also managed to throw their leader, Taichi, back to the real world, resulting in the break up of the team left behind in the Digital World. He did it by dying, mind you, but that was a lot better than his predecessor Devimon did. He comes back and kicks off the series's Running Gag of killing Leomon at least once a series.
Pinocchimon and Piemon are silly, fun-loving, Mega level sociopaths. The latter gets bonus points for also being a Monster Clown.
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 her true shinigami form. Throughout the show, she spends a lot of time being essentiallyawalkingpunchline. It's very easy to forget that she's capable of killing people in cold blood, and that she'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.
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 harmless weirdo who keeps accidentally hypnotizing himself or humorously disagrees with the protagonist about the taste of a pie or just plain looks and/or talks 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.
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.
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.
Rurouni Kenshin has Kenshin, who is usually a polite, obvious moron ... and, if you push him too far, the legendary assassin Hitokiri Battousai.
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 all those years ago. And be warned, he 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.
Fay D. Fluorite from Tsubasa Reservoir Chronicle is a big source of comic relief, but when push comes to shove, you don't want to be pitted against an insanely powerful, well-trained mage who knows hand-to-hand combat and is skilled with a crossbow.
Batman's 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.
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 we see her 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.
And 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 DC Universe. 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.
Deadpool. A madcap goofball with weaponized Yo Mama jokes who thinks he's in a comic book and has conversations with his thought captions. He is also insanely good with every weapon known to man, sometimes to the Bullseye level where it's pretty much a superpower, and he has Confusion Fu going for him, as well as a Wolverine-classHealing Factor. He is an exceptionally deadly fighter and you really would rather have him on your side (though on his side tend want him to just shut up already even if he is the best they've got. Even Galactus could only take so much.)
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 villians not only is he the one who survives, but he survives Jenkins. Nobody else has been able to do that yet.
Fan Fic
Mukrezar is a whimsical, funny, likeable guy with a less-than-perfect record for succeding in his many, many schemes. He is also one of the most cruel and sadistic Keepers.
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 Willy the Giant. In the first scenes of Mickey and the Beanstalk, Willy is introduced as a terrifying kleptomaniac who seems more stormcloud 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. 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 Willy gets really riled up, he also wields an iron morning star the size of a two-story house.
Film — 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.
Several of the characters in Tim Burton's Alice in Wonderland, perhaps most particularly the Mad Hatter, fall into this trope.
Literature
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.
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.
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.
In AnimorphsSixth 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 Blood Knight 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.)
Live Action TV
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.
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.
Professional Wrestling
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 BlueMeanie, 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).
Video Games
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.
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 (apparently it didn't stick) 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 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.
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?
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 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 of Super Mario Bros 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.
For a very clear example, see Mario And Luigi Bowsers Inside Story, about half of which you spend playing as Bowser. Even though for most of the game he has Mario and Luigi helping to power up his body from the inside, he's shown to be a very powerful fighter. In fact, enemies that weren't too difficult for Bowser to pummel into submission become borderline Demonic Spiders when Mario and Luigi try taking them on!
At his least dangerous, Bowser is a super strong fire-breathing turtle monster. He usually has an army complete with armadas of airships, and has a knack for finding and using powerful artifacts. Even when he's being Too Dumb to Live, he's still too powerful to die, as even being immersed in lava just results in him coming back as a skeleton in the bonus levels. Laugh all you want, but remember that he's invaded countries on a whim and everyone that's tried to steal his place as the final boss has died for it.
Arguably, 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.
All the villains of Super Paper Mario are pretty silly, especially the true Big Bad. They plan to destroy the multiverse, and succeed in destroying at least one universe.
The original Silly Villain was Garland "I will knock you all down!" from Final Fantasy I. Who knew that the very first boss you fight would wind up being the final boss, Chaos, in a hugeEvil Plan?
Kefka of Final Fantasy VI. Over the course of the game he goes from a cacklingnutjob in clown makeup, with fairly unremarkable combat abilities, to a Physical God (but still a cackling nutjob in clown makeup, with the exception of the final boss fight).
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 an Arnbjorn 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.
A heroic example: Tyrell from Golden Sun Dark Dawn is blatantly set up as the bumbling sidekick. He starts the game by getting into trouble over his head and breaking valuable equipment, he makes fun of the bad guys' names, he identifies an extinct settlement as such by the lack of food, and he flips out and attempts a No-Holds-Barred Beatdown on Arcanus. Wait, what?
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 modrons in Planescape: Torment are practically comic relief, behaving like socially awkward and poorly programmed robots that are very easy to kill. Then you get hit by the Mechanus Cannon spell for the first time - the first spell to get its own cutscene - and they cease to be as funny: https://www.youtube.com/watch?v=XUjvJP1gOMc.
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.
Solt and Peppor of Chrono Cross are the Quirky Miniboss Squad, He Knows About Timed Hits, and Goldfish Poop Gang all rolled up into two rather silly and bumbling brothers. That is until they call out their superior, Karsh, for the murder of Dario, upon which they drop all the silliness and become a genuinely challenging boss fight.
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 Symphonia has Zelos, team Butt Monkey and The Casanova, turn on you last second and hand Colette over to the Big Bad. In a way, this scene can double as a Beware The Silly Ones for the villains; they, too, underestimate Zelos, and in certain paths that enables him to save the entire party and rejoin you with a key plot item.
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.
Webcomics
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.
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.
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 in The Order of the Stick 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.
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.
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.
Web Original
At times, Dr. Insano of The Spoony Experiment and Atop The Fourth Wall seems like an Ineffectual Sympathetic Villain, but there have been times where he's been a somewhat legit menace, such as the times he took control of the giant robot Neutro, discovered the Anti-Comic Equation (with Warrior #1, a comic so irredeemably awful it distorted the space-time continuum), and hired Squall to assassinate Spoony. Despite all this, Spoony still let him assist him with the review of the awful film, The Clones Of Bruce Lee.
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 Evil League of Evil in Dr. 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.
The platypus is Mother Nature's way of saying, "I made this thing out of spare parts I found on the workshop floor, and it can still fucking cripple you."
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, but 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 Brothers 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.
Turtles Forever explicitly spells out that he and Krang are sitting on technology powerful enough to completely take over the multiverse if used by someone with brains.
Skeletor from the early 80's FilmationHe Man And The Masters Of The Universe cartoon 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.
An episode of Phineas And Ferb had a Bad Future that occured after Candace manages to bust her brothers, which also results in Perry being taken out of commission for a few months. Without anyone to oppose him, Dr. Doofenshmirtz manages to Take Over the World (or at least the Tri-State Area, it's not really clear). Admittedly, the actions of Moral Guardians helped him, but not being opposed was still a factor.
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.
One Justice League Unlimited episode 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 Physical God 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.
One episode of AladdinThe 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. Did I mention that Chaos is a silly blue cat with wings? Did I also mention that he has more power in his whisker than a palace full of genies, can conjure up his own wishes, was able to poof up an Evil Knockoff that Aladdin was forced to fight to a near standstill when he expressed distaste in the cliche of him always winning against his opponents in the series, shrunk Jasmine to the size of an insect and nearly getting stepped on by her own husband when she actually tried to order him to stop his mischief, and actually TERRIFIES Mirage, who if you didn't know, is an Evil Elemental who has proven many times 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.
