Chuck, in Panty & Stocking with Garterbelt. In the last episode, Chuck unzips himself to reveal this... THING◊, and proceeds to charge straight up the huge Ghost, taking down Fastener (who does something similar, turning into a two headed dragon) along the way.
Midway through Higurashi no Naku Koro ni, Hanyuu decides to get serious: "I have finally realized that this cycle of suffering is because of your Will. WE WILL NOT LOSE TO YOUR WILL!"
Even after that, in the last few episodes, several of the normally useless adults have these kind of moments, with Kasai intimidating a group of mooks into submission with a large shotgun and Mr. Delicious judo-flipping a corrupt superior officer. These are all trumped royally when Akasaka shows off his shiny new levels in badass.
At first acquaintance, Rock of Black Lagoon seems harmless and nice, a contrast to his Darker and Edgier crewmates, not to mention the city he lives in, a Wretched Hive. Then, just when you think you're going to win, he shows why he's a member of the Black Lagoon crew.
Really shows up in the Baile de la Muerta arc. He just pushes a couple of people in the right directions and sits back and laughs. Literally. Also when he shows his Slasher Smile, and that, no, he really isn't very idealistic at all (contrary to what everyone else thinks).
Vash the Stampede from Trigun lives and breathes this trope. 90% of the time he's goofing off, playing with local children, or even getting into trouble with local thugs, but when the chips are down, he really does live up to his nickname of "The Humanoid Typhoon". This is usually when he puts hsi sungalsses on.
For the entirety of the first episode and the majority of the second episode, the girls are doubtful that they've found the actual Vash, because he's such a buffoon. Towards the end of the second episode, though, the villain shoots at him and instead of panicking and scurrying away (which is what he did in Ep 1 when being shot at), he just takes a half-step to the side and gives the shooter the Thousand-Yard Stare. This is really the first clue that just maybe this guy's reputation as a badass isn't entirely undeserved.
Macross Frontier contains a direct subversion when Sheryl Nome attempts to fly a Valkyrie for the first time during a battle. She even intones her Catch Phrase and gets a Theme Music Power-Up, but she botches the whole thing as one might expect of an Idol Singer, getting shot down almost immediately.
Madlax, Elenore beating (more accurately kicking) the daylights out of a male classmate of who attacked Margaret.
Done all the time in the Yu-Gi-Oh! franchise. A duelist will be seen as weak and puny and will spend a turn or two making bad moves. Then suddenly, they'll reveal their weak plays to be part of a master strategy, they'll pull out a super combo that pushes the opponent into a corner, and now every move they make will just push them further in. This is usually accompanied by a minute or two of the character taunting their opponent for playing into their hand and explaining their combo in great detail to emphasize how powerful it is.
Joey in particular demonstrates this trope a lot. Most of the time, he's the Plucky Comic Relief far outshadowed by his King of Games best friend, who, after all, has card-playing superpowers. But every once in a while, when you push him up against a wall, or you threaten the well-being of his sister, Mai, or Yugi, his eyes become little windows to hell, and you'd better brace yourself for a hard smackdown; he's Yugi's Lancer for a reason. The only time this has failed is his duel against Marik, and he managed to (mostly) withstand an attack by an Egyptian god and get Marik to practically crap his pants before collapsing mere seconds before winning the duel.
Mokey Mokey is a 1-star (i.e. incredibly weak) monster... until it gets mad, at least. The card description says that "sometimes he gets mad and that is dreadful," and it's serious - just play Mokey Mokey Smackdown and wait for one of your Fairy-Type monsters to be destroyed. All of your Mokey Mokeys get ten times their normal attack power for the rest of your turn. One character - Belowski - uses a strategy involving destroying his own Fairy-Type monsters to start the "smackdown".
Not to mention Yugi himself. In the second series, to a minor degree — whenever Yugi's friends are threatened, expect a very pissed Yami/Yugipossession...symbiosis...thing... to kick ass and take names (or whenever Yugi duels in a tournament; card games are serious business!) — but it shows up in a very big way in the first series. Basic plot: Enemy of the week bullies/belittles/generally makes life a living hell for Yugi or one of his friends. Yugi just sort of takes it, until things go too far even for him. Enter Yami, ancient Pharaoh, master gamer, total sociopath. Three words, season 0 watchers: "It's game time." And God help the baddie who cheats in a Shadow Game...
In Yu-Gi-Oh! GX, you know Kenzan (Hassleberry in the dub) is done kidding around when his eyes turn reptilian; that's when the dinosaur DNA inside him is about to kick in, and he gains his Heroic Second Wind. (Not that his record as a duelist was all-too good, but he did manage to accomplish quite a few things without that.)
The cast consists of children in possession of potent, possibly lethal "ninja" powers. During Orochimaru's Invasion, the children are sent after The Dragon while the adults, with assistance from Legendary Sannin Jiraiya, repel the entire invasion force after most of Konoha's military forces were lulled to sleep.
When Tobi is first introduced, he's The Load with a tag-along, singsong personality and is probably the least threatening member of his organization. As it turns out, he is not only the Big Bad, but the reason he survives the way he does is because he can phase himself through another dimension.
The first scene in which Might Guy pulls out nunchucks. He goes from Plucky Comic Relief to Crouching Moron, Hidden Badass in seconds. However, his goofy personality still remains. What arguably might be his moment in the spotlight was when he struck an enemy assassin through a waterfall, believing that the fleeing enemy was actually his inner self, which he sought to defeat.
The latter half of Digimon Savers has plenty of awesome from Satsuma, Miki, Megumi, Yushima, and their partners. Unfortunately, while it is revealed that Yggdrasil strictly forbade Kamemon and Kudamon to fight while they observed the humans, lines like "It's about time we showed off our Perfect levels," don't exactly dispel the Fridge Logic.
Shinkuro from the anime Kure-nai. After 11 episodes of all but getting his ass handed to him and looking incompetent, he finally decides to fight for real in the finale, easily kicking major ass. It then culminates with him seeing his mentor/boss get stabbed, which triggers him into fully releasing the assassin's blade surgically placed inside of his arm. He goes into a mindless killing rage, using previously unseen insane skills, wiping out the guy who did it in under a second.Daaamn...
While Kurenai Shinkurou does qualify (he has some martial arts training, but his peers are far superior), similar occurrences happen earlier on. Additionally, the blade appears involuntarily and Shinkurou says outright he doesn't want to use it. However, damn is right.
In Family Compo, Uncle Sora mentions that his father is the one that taught him kendo. A few chapters later, he uses a massage stick to open a can of whoop-ass on some invaders of the house.
Nausicaä of the Valley of the Wind gives us Lord Yupa, a kindly old bearded guy, sweet with children, loved by all. Then he lands on an enemy battleship, whips up two blades, and starts cutting terrified mooks apart.
One episode of The Big O has Roger's mild-mannered butler Alfred Norman pulling a huge, belt-fed gun out of Hammerspace to protect his employer and his robot girl sidekick. Then, when he's run out of big guns, he whips out twin semiautomatic pistols, fires them straight overhead, shredding a few robots about to land on him, all in the time it takes to yell "Sons of bitches!"
Several comic relief characters from Dragon Ball fall in this category. Master Roshi started out as a purely comic character (introduced as a pervert with a pet turtle); only later did he reveal his fighting skills. Yajirobe was instrumental in defeating Vegeta, and several Big Bads came to regret underestimating Krillin. Even Mr. Satan has his moments — he's worthless against ki fighters, but he can take down any human thug with ease.
Are you kidding? At the end, he risked his life to save Vegeta and even helped give Goku the power he needed to take down Kid Buu.
There's also the fact that he was able to make himself Majin Buu's Morality Pet. Buu would have been fully redeemed if not for those idiot bikers gunning Mr. Satan down.
Even Goku himself can come off like this, often joking and light-hearted even in the midst of battle. But when you actually piss him off? You are done. Period. This even shows in his English VA, as the tone in his voice clearly changes to show he's dead serious.
Magical Girl Lyrical Nanoha Striker S: When faced with the destruction of her new home and death of her friends, Caro, the supporting healer of the group, summons a Godzilla sized dragon that proceeds to wipe the floor with the bad guys.
From the first season: Chrono Harlaown. We'd been getting vague hints about his skill with magic, despite being confirmed weaker than the protagonist, but he never seemed to actually do anything, and the relative strength level of the other TSAB mages wasn't helping his case. Then, in the finale, he obliterates several dozen Mecha Mooks in a single attack without the slightest effort, leaving Nanoha and Yuuno gaping. And before that, he goes One-Man Army, Storming the Castle that previously swallowed a troop of hardened adult officers (Chrono is barely 12 at the time) and spit them out.
The quirky father, Isshin Kurosaki, confronts Grand Fisher, and reveals that he was once a Captain level Shinigami. He then kills Grand Fisher, who had evaded capture and defeat for over fifty years, with a single attack.
Hellsing. Walter C. Dornez is a rather benign butler who nonetheless displays some technical wizardry with weapons. When vampires attack the compound, however, he reveals himself to be a Retired Badass and goes into full Battle Butler mode, slicing through squads of mooks at a time with his Razor Floss.
In Soul Eater, it is very easy to discount Shinigami-sama as harmless Mission Control, what with his goofy mask, silly speech pattern, and Verbal Tics, and his tendency to spend most of his time inside the central chamber of Shibusen and doing Boke And Tsukkomi Routines with his Death Scythe. Then the Kishin imprisoned under Death City breaks free, and Shinigami is allowed to show the cast just why he's considered a Physical God: His Megaton Punch does have some combat-related ability, for one...
Spirit gets this during his and Stein's fight with Medusa, in a moment of Mood Whiplash where he muses about removing her white coat and promptly points out that, being the Death Scythe, he has to kill her. He is also eager to fight Asura with Shinigami in the anime.
Younger shinigami, Death the Kid, has shown off what happens when he takes fights 'seriously' without breaking down into OCD-driven mass destruction. With a little help from his dad (essentially, given what the Sanzu Line thing did to Shinigami), he goes from missing an arm and very close to Mosquito killing him, to fighting on a par with the vampire. He didn't exactly win, but he didn't lose either. And his arm got reattached.
It's worth mentioning his two weapons, Liz and Patty. They act like his retainers and are generally both cheerful, laidback girls. But mess with them and they'll be very happy to show you just how they managed to survive most of their lives on the streets of New York.
Black*Star gets a lot of this as well. Once he manages to calm down his I-Will-Surpass-The-Gods complex and fight seriously, he's one of the most frighteningly competent characters in the series, even being called the current strongest meister in the Academy and breaking Kid out of insanity by literally beating it out of him.
The main characters of Mahoujin Guru Guru are easily distracted, to say the least. But both Nike and Kukuri have managed to perform some fine feats of fighting evil when the need arises. Especially when one or the other are in danger.
Chichiri and Nuriko from Fushigi Yuugi both tend to be comic relief, with Chichiri sticking to the "religious" side of Religious Bruiser and Nuriko a sassy Wholesome Crossdresser. Except when you need Chichiri to single-handedly get you out of the enemy stronghold, or when you need Nuriko to take on a ferocious wolf-man, and they reveal their heights of badassitude.
Hare from the Monster Rancher anime was generally portrayed as competent, but on more than one occasion, his own arrogance would result in his plans failing dramatically, forcing him to improvise. Thus focused, his IQ would practically double.
Black Butler. Holy crap. Do not mess with the Phantomhive servants. Just... don't.
A lot of characters from Saiunkoku Monogatari. Normally childish, goofy Ryuuki turns out to be only pretending to be an idiot for a variety of complicated reasons and manages to take down several highly trained assassins to save Shuurei, in spite of his fear of the dark and, oh, not being able to see; Shouka, Shuurei's blundering, spacey father is actually the legendary assassin Black Wolf, and... well, just don't hurt Shuurei and let him know about it; Ryuuren the eccentric genius manages to take down bad guys by the dozen using only his flute; and even the little brainiac Eigetsu turns out to have a split personality, and his other side is an insanely good fighter. And that's just the tip of the iceberg; don't even get me started on the women....
Miss Maria: It's shameful that, even in my old age, I still have to show this graceful form.
Doubles as a Never Mess with Granny moment. Especially since she's been getting provoked by the invaders since the start, and her patience just reached its limit.
Nanael from Queen's Blade is a ditzy angel who always gets in trouble and can't even fly straight, because of her asymmetric wings — until the moment she beats up three of the most badass characters without even breaking a sweat.
Generally, when Luffy cracks his knuckles, Zoro puts his bandana on his head rather than around his arm, Sanji lights a cigarette in the middle of a fight, and Robin brings her hands up to the opposite shoulders; when they do these, you know they're taking their fight seriously.
Kaku even lampshades Zoro's bandana.
Kaku: Are you supposed to get stronger when you wear that bandana on your head?
Zoro: Let's find out.
Also, pretty much any time pre-Time Skip that Luffy goes into Gear Second, Sanji goes into Diable Jambe, and Chopper eats his Rumble Ball...though that last one is even more Let's Get Dangerous post-Time Skip.
When Usopp and Luffy fight over ownership of Merry (it was about to be decommissioned), Usopp, who had just been beaten senseless and is covered in bandages and bruises, goes crazy. The first eight minutes of that fight is nothing but him flooring Luffy with everything he has. He still is taken down with one hit, though. The one hit that connects, that is. Luffy's first solid punch gets absorbed and reflected by an Impact Dial, courtesy of Usopp.
Usopp plays this trope magnificently in Thriller Bark when he calls out for help, then rescues himself as Sogeking complete with gag theme turned Crowning Music of Awesome.
In the Thriller Bark storyline, Brook was introduced as a bumbling socially incompetent idiot. Many chapters later, he suddenly had one of the creepier dramatic entrances of the series and one-shotted a giant monster who was wiping the floor with Franky and Robin at the same time.
In the opening first Chapter, Shanks and his crew just seemed to be cheerfully messing around, and got chewed up quite a bit by Higuma. When Shanks laughed it off, the latter assumed he was just a weakling. A bit later, he kidnapped Luffy. And then Shanks shows them just how bad an idea it was to mess with him, with his crew decimating Higuma's bandit force, and Higuma himself fleeing, only to be eaten by a sea monster, the implication being it's the sort Shanks deals with almost every day.
Though he gave Sanji a good fight in the Alabasta arc, Mr. 2 Bon Kurei was generally considered a joke both before and after his Heel-Face Turn. Then he reappears in Impel Down, and fights off a pack of the highest level prison guard "mooks". With his bare hands. In sub-zero temperatures. Half naked. To save the main character's life. Sure, he had to have some skills to be the second strongest fighter in a major criminal organization, but with how much Obfuscating Stupidity he did...damn.
Not to mention that at the end of that arc, he stays behind in Impel Down to give Luffy and his new allies the chance they needed to escape. Putting in perspective, this has him facing a large group of armed guards and the prison's warden, the latter having used his Doku Doku no Mi (Venom-Venom Fruit) powers to send Luffy to death's door, EFFORTLESSLY, a few chapters earlier, alone and unarmed with anything but his martial arts. The battle may never be seen, but post-Time Skip it's revealed that he somehow survived the fight and is alive and well, living in Impel Down's secret Level 5.5 as the new ruler.
Last but not least, from its first introduction to near the end of Punk Hazard Arc, Franky Shogun was shown as a unnecessary giant robot that serves mainly for comic relief and to impress the immature male members of the crew. This is for good reason as most of the attacks come from Franky himself. Robin even lampshaded on this by asking what the robot was even for. Then we found out how FREAKING TOUGH and dangerous it is. While its physical strength is unquestionable, it was also actually quite agile for its size as it was able to punch CANNONBALLS back at Baby 5 and deflect her spinning attack . To make it even better, Franky Shogun even has its own much more powerful version of Franky's Weapon left, and a ON-LAND VERSION of the freaking GAON CANNON!!!. Hell, you could say that the enemies back at Fishman Island were not strong enough for him to use Shogun seriously.
Happens at the beginning of Ninja Scroll: The Series. Shigure is always getting angry at her fellow villagers about their inability to take their martial arts training seriously — it turns out that the entire village is made up of skilled fighters whose sole job is to protect her, and who were only pretending to be lousy at it. Unfortunately, even they all get wiped out by an army of demons, so she has to flee.
Folgore and Kanchomé are normally comic relief in Konjiki No Gash Bell, winning all their battles through tenacity alone. However, in the manga, Clear Note's threat prompts Kanchomé to begin training, and discover that he has the strongest power in existence: Illusion. It's hammered home when he locks Gomu in an illusion where he is constantly tortured; only Folgore himself can calm Kanchomé down. Later, Gash wins the final battle through Kanchomé's direct help when the latter makes Clear Note believe he destroyed the Earth, when it was only an illusion Kanchomé created that was destroyed. And, of course, with this newfound power, he was actually able to beat Gash in a sparring match.
Also, in the Pokémon anime, Misty's Psyduck. Normally totally useless, but whenever it gets a serious headache, it gains amazing psychic powers.
Misty's Togepi. The little ball of cuteness that can barely walk on its own packs a mean Metronome attack which saves the day almost every time it uses it.
Ash turning his hat backwards might also count in the earlier episodes, although he's done it once or twice recently as well.
Mew in Pokémon: The First Movie, spends most of the film curiously swooping around in a playful manner. Mewtwo attempts to goad it into a fight, and it ignores him. However, after one of his energy attacks successfully hits Mew, sending it flying into the sky, it drops its playful manner entirely and fires an attack back at Mewtwo, blasting him backwards through a wall. After this, it ceases to be cuddly and engages in a massive and vicious battle with its clone Mewtwo.
Yellow from Pokémon Special. She is sweet and pacifistic to the degree it pains her to hurt enemies (a psychic empath), even if it means more trouble for her, not to mention she's a terrible battler and her Pokemon's levels are rather laughably low compared to the other Dex Holders. However, push her to the edge enough and her Pokemon's levels get boosted up to the point that she can take down just about anybody. (This phenomenon has been scientifically measured, their powers are roughly tripled to quadrupled.) Lance got his ass handed to him and Sird/Storc wisely decided to make a run for it before Yellow got the chance to do the same to her.
Paka and Uji, Platinum's real bodyguards, are a pair of goofballs who have a penchant for corny posing. Put them in a fight, and they show that they are a pair of goofballs who have a penchant for corny posing along with a strong work ethic and equally strong battling skills.
Any time this music plays in Umineko no Naku Koro ni, it's a sure sign that Battler is about to be way, way more awesome than anyone expected. This means doing something like completely ignoring the most powerful attack the Siestas can throw at him. Other human characters also have Hidden Depths of badassitude, but he's the only one to have a separate theme song for them.
Erika and Walker of Durarara!!. Not only are they Dollars, the were also instrumental in the downfall of the Blue Squares Gang, which they accomplished by pouring gasoline on the leaders of the Blue Squares and lighting them on fire.
Generally, Gintoki doesn't need more than the wooden sword he bought in an infomercial to slice and dice his enemies, alien airships, towering mechas, and so on. There are at most two or three enemies in Gintama whom he deems strong enough that he decides to swap his wooden sword for a real sword in the fight. However, you'll know that he still doesn't consider his enemies challenging until he starts dual wielding.
Matsuda shooting at Light in the final episode of Death Note
Many characters in Ghost Sweeper Mikami, but most notably Yokoshima, the perverted Butt Monkey of the series. While he is treated harshly by his employer and also get sthe worst of everything, when he does get serious, he can really cause some mondo damage. Hell, he winds up taking down Medusa, once of the series' biggest bads, not once but twice.
In Tiger & Bunny, Kotetsu/Wild Tiger has shown himself to be a complete dork and something of a klutz. However, dork or not, he's still a veteran superhero (and, according to Yuri Petrov's archived data, a former holder of the King of Heroes title) and demonstrates quite regularly that he can be quite a badass dork.
Origami Cyclone as well. This is a guy whose main style of 'heroism' is to pop up everywhere there's a camera, largely because he doesn't think his superpower measures up to the other heroes. Later in the series, after a boost of confidence, he proves to be much more badass than he had been before, using his power to disguise himself as a wanted poster at one point, and proving that he really can fight in the finale.
And his infiltration of the Ouroboros base, which took guts and was almost a Heroic Sacrifice once Jake found him.
Xerxes Break of Pandora Hearts says this almost verbatim toward the end of the anime. Although he has revealed to the audience how truly terrifyingly badass he is during earlier fights, none of the main cast have seen him do it until that point, and their reaction is little less than speechless shock. To top it off, every time he gets dangerous, he does so without changing his overly flamboyant behavior and speech.
In the Axis Powers Hetalia movie, everyone pulls one of these; given that almost nobody in the entire cast is usually serious, this is something of a welcome change. After the heroes have been stranded on an island, the alien mothership lands and deposits a very large army of facelessaliens around them, who respond to this threat by punching the crap out of it. Especially awesome moments include America remembering he has super strength and backflipping out of the way of several shots, Russia facepalming the aliens out of the way note One for you, one for you... and Japan picking up a stick to wield as a katana. Sadly, they still lose, but even that has its fair share of epic moments; for example, when Germany realizes everyone else has been hit:
"All right then, come on! I'll kill you all with my bare hands!" *proceeds to take down another dozen before finally getting taken down*
In Detective Conan, Kogoro is a bumbling private investigator who suffers from being Brilliant, but Lazy. Instead of actually working on cases, he prefers to hit on pretty women, gamble, and drink lots and lots of booze. There are a few things that will spur him into genuine competency though, mainly Ran and Conan being put in danger. A specific example is shown in one of the movies, when a flashback reveals that his wife was taken hostage in front of him. Without flinching, he frees her by grazing her with a bullet, causing the criminal to toss her aside and leaving said criminal open to be directly attacked.
Rushuna Tendou of Grenadier. In the first episode, she looks like she's going to be the comic relief, while Yachiro the samurai is fending off bullets with a sword. Then, when she tries to get the castle full of heavily armed villains to release the captured lord and is rebuffed, the comic vanishes. After she says, "In that case, you don't get a smile," she demonstrates why she's considered the Distaff Counterpart of Vash the Stampede.
Mitsuko Kongou of A Certain Scientific Railgun. Vain, boastful, and generally seen getting embarassed or beaten up. Then, come episode 23, she finally gets into a situation where she can see her opponent and use her powers. Immediate cut to the Big Bad being informed that a Power Armor squad has been taken out. The next episode marks her first on-screen power use when she punches a truck into a pair of attack helicopters.
Kuroko as well. Most of her screen time is spent trying to get into Mikoto's shorts, but whenever there's a crisis, she immediately switches from Loveable Sex Maniac to an extremely competent law enforcement official.
Hikaru is a cute, innocent Genki Girl, but as soon as someone tries to hurt her friends, she will burn them to a crisp.
Eagle Vision in Rayearth II is a smiling and affable fellow... until he gets into his Humongous Mecha. He's capable of fighting the Magic Knights and other countries to a standstill.
Near the end of Vampire Knight, it is revealed why, exactly, Cross Kaien is called the greatest Vampire Hunter still alive, when he dusts off his old sword and takes off his glasses.
Achika in the first Tenchi Muyo! movie, Tenchi Muyo in Love, was just an Ordinary High-School Student who had no idea why KAIN, a Sealed Evil in a Can, was targeting her at all. Then, he made the mistake of harming Noboyuki, the two of them harboring crushes on each other. This was enough for her to unlock her incredible power as a royal blooded Juraian, the thing KAIN was trying to kill her for. Oops.