The Joker is more known for being murderous and unpredictable than being an amazing hand-to-hand fighter, with only a handful of adaptations showing him as any physical match for Batman. But for The Batman, he was given enhanced strength, agility, and dexterity. In the first episode he was climbing all over the place like a monkey, though this was toned down in subsequent appearances.
The Penguin is likewise an exceptional combatant, a far cry from his usual portly, unathletic portrayal.
This is more a case of Olderthan They Think, as Depending on the Writer the Penguin has been written as a skilled judoko and a physical match to Batman, while other writers elect to use the above interpretation, often for easier story telling.
Justice League Unlimited gave this to Aquaman compared to Superfriends (the comics version was always pretty badass). They ended using almost any "joke" character in the past to great effect.
The Terrible Trio were a trio of rich brats who wore animal masks and got rather lucky against Batman. However, they crossed the Moral Event Horizon so well by the end of the episode that followup series brought them back. In The Batman, they were social outcasts at Gotham University who stole the Man-Bat formula and became werebeasts for Batman and Batgirl to fight. In Batman: The Brave and the Bold, they are were Arrogant Kung Fu Guys who betrayed and killed their master, controlled a clan of Shadow Ninja and planed to take over the city. Oh, and they also stole a talisman that turned them into werebeasts too.
Mr. Freeze was originally just a campy cold-themed villain from the DC Silver Age, and had been killed off by the Joker in the comics years before B: TAS. His appearance as a more serious Anti-Villain with a Dark and Troubled Past gained enough popularity that he was brought back in the comics, with his backstory retconned to more closely fit the animated version.
Beware the Batman does this to Alfred Pennyworth, playing up his experience at MI6 from the comics and actively helping train Bruce Wayne and Batman for combat (his first scene in the pilot has him staging a mock attack on Bruce to gauge his readiness, and calculates the number of strikes it took and should have took to subdue him). He also helps Simon Stagg and Michael Holt escape from Professor Pyg and Mr. Toad; and even manages to pull a shotgun on Silver Monkey when he invades Wayne Manor.
On the villain side of things, Cypher goes from being a plains-clothed hypnotist to a stealthy cyborg with a rather creepy method of mind-control.
Spider-Man villain Electro could get pretty lame in the comics, with his power just about enough to almost kill the web-slinger once before getting beat every time after. In Spider-Man: The Animated Series however, he was a Big Bad by the last episode of the story arc in his first appearance, replacing the Red Skull as the primary threat. The guy then easily dispatched the Six American Heroes (a team of Golden Age heroes which included Captain America), the Insidious Six, and Spider-Man, and made it clear he could kill any of them at any time, took control of the Earth's satellites through the electrical signals he fired to broadcast himself to the world's media, announce he's the new President Evil of the world, and when all of S.H.I.E.L.D. chose to disagree, he handled them single-handedly by shooting down their base:
(Nick Fury jumps off the collapsing S.H.I.E.L.D. base, then pulls his parachute)
Female S.H.I.E.L.D. Agent:(on Nick Fury's earphone) Agent Nick Fury, do you copy?
Nick Fury: I copy, what it's worth. He took down all of S.H.I.E.L.D. with only a gesture. Heaven help us all.
(S.H.I.E.L.D. base crashes in the sea then explodes)
The series turned the Spot into a genuine threat, capable of running rings around Spider-Man with his ability to create masses of portals.
Comics-verse Black Cat is a Badass Normal who occasionally wields bad-luck powers. Here, she starts out as a classmate of Peter's before gaining powers from the Super Serum that created Captain America.
Ultimate Spider-Man does the same to its version of Electro. Starting out like his B-list comic self, he gets upgraded into being more like the Ultimate and 90s cartoon versions, with unlimited control over all things electrical within his range, and his range seemed to be "everywhere". If he'd been capable of saying "screw fighting you guys, I'm gonna Take Over the World; good luck punching living electricity!" he could have done so. His real weakness, established throughout the episode, is that for all his newfound power he still thinks like a B-list hood.
The Sandman took the ability to add the sand around him to himself to its logical conclusion. You know why that island you're on isn't on any map but SHIELD's, with a "seriously don't go there, for reals" warning? Every single bit of soil on the entire island is him, making it a Genius Loci that doesn't like you. Taking the smallest bit of him - oh, like the dirt on your clothes after you think you're done fighting him - back to the mainland would be bad. Using no powers he doesn't have in other continuities, just being smarter about how he used them and having a reason to be really pissed, it was very nearly "arrivederci, North America."
Teen Titans made Aqualad a badass, water-bending Atlantean cop who was lusted after by Raven and Starfire (for one episode, at least). Not too bad considering he was written out of the original Teen Titans comic book because the writer thought he was useless.
Raven as well. In the comics, she can simply teleport, heal other people, and sense other's feelings (nothing actually useful during a fight). Here, she uses telekinesis, can fly, knows sorcery, etc.
Killer Moth. In the comics, he's the most ineffectual of the Ineffectual Sympathetic Villains with a completely ridiculous costume that looks like it was put together by a colorblind tailor. Here, he's a half-man, half-moth hybrid with an army of genetically modified bugs at his command.
Kid Flash also counts. In most incarnations, they have to work around his Story Breaker Power of Super Speed. Here, they take it and use it to his full extent, and he spends most of the episode literally running circles around the Hive Five. The only way they manage to bring him down is by tiring him out, and even that takes a long time.
Madame Rouge. In the comics, after a short tenure as a recurring villain, she winds up Killed Off for Real and a source of guilt for Beast Boy. Here, her powers (stretching, Human Shifting) are greatly upgraded. Nothing hurts her, except heat, and even then she just has to take a second to shapeshift into an undamaged form. The episode with Hot Spot alone being hunted by her makes her almost scary, and when she returns to battle Kid Flash, she's every bit as Badass. He runs circles around the HIVE Five and looks so good doing it... then she shows up and it's a whole 'nother story, able to shift fast enough to actually stretch out to grab Kid Flash when he's looking like a yellowy blur and then proceed to lay down a beatdown.
Later games struck a middle ground, where he's generally competent but almost always gets pushed aside by the game's final boss, which is usually something he built / freed that went out of control. While as buffoonish and comical as ever, he has actually posed even more of a genuine threat and eventually regains the role of final boss.
Bumblebee, once again, featuring in Transformers Prime. His first foray into robot combat in the pilot episode had him coming to Arcee's aid by driving off an overpass, transforming, landing with a thud and by the next beat his fist connects with an Vehicon's face. He doesn't appear to be quite the same bruiser as in the movies, but he is no less reliable.
Generation 1Starscream was pretty much a Running Gag of one transparent backstabbing plan after another, often openly telling Megs what an idiot he is and how Starscream should be in charge, and only being kept alive because his Megatron was no brighter than he. Certainlaterincarnationshowever are nigh unto Magnificent Bastard class, and the second-most-powerful Decepticon next to Megs himself to boot. At one point in Transformers Cybertron, he borrows a portion of the power of the god Primus and spends an arc handily kicking around all the Autobots and Decepticons singlehandedly.
Megatron himself. G1 Megatron was Too Dumb to Live when it came to Starscream, and would trust him again ten seconds after being shot at by him. "Decepticons, retreat! RETREEEEEAT!!" was practically his Catch Phrase, and even the series' most diehard fans admit that he'd yell it when the going got tough even if he still actually had the upper hand. Oh, and he turned into a gun that couldn't move or fire himself and was usually held by... go on, guess who. Since then, he's had highly Badass vehicle and beast modes, and has been freakishly powerful and/or a brilliant Diabolical Mastermind.
Both Starscream and Megatron have outdone themselves in Transformers Prime. The latter's a soulless Bad Boss who coldly tortures his enemies and allies, and plots to use his Necromancer abilities to raise the dead of all Cybertron as an army. Starscream, not to be outdone, has become a sociopathic Bastard Understudy who casually murders a named character in the first ten minutes of the show, and successfully betrays Megatron some episodes into the series.
Arcee, who in most incarnations is presented as just The Chick, here is presented as a badass Action Girl.
Wheeljack in the original cartoon he is presented as something of a Mad Scientist archetype, edging into Gadgeteer Genius due to his tendency to invent things (and build the Dinobots). This carried over to similarly named, similarly-designed characters in both the movies and Animated series. Prime, however, turns him into a Dual WieldingRogue Agent with a love for mayhem and explosives, an ace pilot, and a former Wrecker to boot.
The G1 version of Soundwave didn't do much to stick out from the rank and file other than have a cool voice and shoot a bunch of minions out of his chest. The Prime version, on the other hand, looks like a mechanical Slender Man, is eerily silent and frighteningly efficient, and happens to be one of the few Decepticons that can give the aforementioned Wheeljack a run for his money.
On the villains' side, the Grim Reaper is definitely far more badass and sinister than his comics version. In the comics, he wasn't a good fighter, was pointlessly racist and non-functionally crazy, wore purple spandex with goofy, Galactus-style head gear, and was pretty much a joke in that regard. In the series, he wears a dark hoodedcape and is a Soft Spoken SadistPsycho for Hire with a Slasher Smile. He effortlessly broke into and out of a prison that was designed by Tony Stark and guarded by SHIELD, and can slash Hawkeye's arrows and Cap's shield from mid-air with his scythe.
Believe it or not, Hulk has this in a way. He's not just the team berserker that they point at something to hit. This Hulk is smarter (think how he was in World War Hulk, for example) unless he's pissed off beyond belief (at which point the villain simply can't win anyway). Notably, there's almost no Hulk Speak to be found, he understands and uses sarcasm, and got Hawkeye to stay with the team by teasing him. And his favorite teammate is Wasp. So if you do hurt her Adaptational Badass self, you get to deal with him.
Klarion the Witch Boy is a full blown Lord of Chaos and arch rival of Doctor Fate in this series instead of being just another magic user. He's still as childish as ever, though.
Mister Twister, originally a rather feeble villain whose powers came from a magic stick, becomes an incredibly powerful android who effortlessly solos the entire team (up to and including Superboy) while spouting arrogant one-liners left and right.
Count Vertigo, instead of being a guy who makes people dizzy, is a power-hungry despot trying to kill the queen of his country who's more of The Chessmaster than anything else. His superpowers are more an afterthought.
The Big Bad of season 2, the Reach are vastly more powerful than their comics counterparts. In the comics they are a weak military force using subterfuge and trickery to take Earth in a century, with an enforcer who could be beaten by a single hero. Here they are a full fleet of warships, and the Black Beetle took out Miss Martian, Superboy, Wondergirl, Lagoon Boy, Tim Drake, Bumblebee, and only Blue Beetle even slows him down. And according to Impulse's future, it only takes them a couple decades to conquer Earth.
Matt Olsen of W.I.T.C.H., prior to the comics turning him in to a failed version of The Obi-Wan. In the cartoons, Matt was a normal guitarist who, after getting fed up with Will ditching him on dates, decided to find out what the hell was going on. After finding out her double life, he decided he wasn't going to stand there and let her get hurt all the time. Not only does he take combat lessons from Caleb, he also gains a massive power boost when he's forced to take up a fraction of the Heart of Earth, putting him at equal (if not greater) footing of Will herself!
Caleb himself is a Badass rebel leader in the series who is much more of a fighter than the original and doesn't spend most of the series as a flower because of Phobos, either. A fan only familiar with the comics who read this page would likely say "back up a sec, Caleb is giving somebody combat lessons?"
His underlings the Mutants (now members of the other animal races populating Third Earth) continue the pattern, with the Jackalman and Monkian analogs Kaynar and Addicus in particular portrayed as vicious, ruthless criminals before being appointed generals in Mumm-Ra's forces, and devastating fighters in battle.
The My Little Pony toy line has always been rather peaceful. However being an 80s cartoon, the original cartoon was considerably darker and more action packed so several characters became more Badass than before.
From the same series, Grimbor & Terra-Man. The former in the comics was just chain-weapon themed villain who sought revenge for his wife's death, while the cartoon one was a skilled mercenary who owned the team (sans Karate Kid). The latter was originally a environmental terrorist who dressed in a cowboy-inspired battlesuit (and was exclusively a Superman foe, no less), while the cartoon version was a Terminator-like robot who was nearly unbeatable.
In the original Teenage Mutant Ninja Turtles cartoon, Rat King is a man who had a connection with rats with speaking to them, but he usually left the fighting to his partner Leatherhead and was quite cowardly. In Teenage Mutant Ninja Turtles (2012), he gains Psychic Powers and becomes a Woobie, Destroyer of Worlds as Dr. Victor Falco, being able to easily telegraph the Turtles' moves in combat and having a mind link to the rats, manipulating Splinter on a much higher level than he did in the 1987 cartoon. It forces the Turtles to "fight without thinking" on their first encounter (something difficult for resident Smart Guy Donatello).
The Fantastic Four (1967) has a minor example. In the original comics, Sue seemed pretty worthless as a crimefighter until the writers expanded her powers from simply turning herself invisible, to also creating invisible force fields and turning other people and things invisible. This cartoon had Sue also use those abilities in retellings of early comics, so that she wouldn't seem too useless.
Iron Man: Armored Adventures did this with Whiplash, prior to his movie incarnation, where he goes from a loser in stupid costume with whip weapons to a cyborg in Powered Armor, who notably in the second season after a Mid-Season Upgrade defeats both Iron Man and Warmachine and destroys Iron Man's original armor. Also done with Justin Hammer, a Non-Action Big Bad in the comics, who in this series has his own armor as Titanium Man.
Everyone in Star Wars: Clone Wars got a huge boost to their power level and even their competency in a lost of places, the most spectacular being Mace Windu (who is already one of the most Badass Jedi ever) slaughtering an entire droid army with his bare hands. Indeed the spectacular destruction committed by the cast is so at odds with most Star Wars "canon" that it's a widely accepted Wild Mass Guess the series is in-universe propaganda.
Oddly enough, done with Warmonger in Mighty Max. Warmonger had only one appearance in the toyline the show was based off of, the playset "Mighty Max Trapped In Skull Mountain." In the corresponding mini-comic Warmonger is depicted as an ineffectual minor villain whose only accomplishment of note was getting splattered by friendly fire from Skullmaster's catapult. In the cartoon he's The Dragon to Big Bad Skullmaster and a capable villain in his own right, who has even managed to stand his ground against resident Badass Norman a time or two.