In the games and most cartoon adaptations, Dr "Eggman" Robotnik is villainous, but with a highly affable and clownish demeanor, and in some cases leans into Anti-Villain territory. Robotnik of Sonic Sat AM and to a lesser extent Sonic Underground, however, is a monstrous (and far less humorous) dictator that not only has taken over most of the planet but thrives almost lustfully on having any remaining civilians painfullyroboticized. This depiction is drifted in and out for both comic adaptations (although they refer to his more petty, comical personality a lot more).
In the comics, Kirk Langstrom created the serum that turned him into Man-Bat to cure his own deafness, but on The Batman, he transforms himself into the Man-Bat out of a desire to be feared. That said, by his appearance in the fifth season, he's done a Heel-Face Turn, saying that he's done with being Man-Bat and even offers to assist in stopping the Terrible Trio.
One example is the Big Bad Anarky. In the comics, Anarky was depicted as twelve year old Lonnie Machin, a political anti-government activist and altruist who saw humanity as naturally good, but with consumerism and big government getting in the way. He wasn't a villain more than he was an anti-hero who even Batman acknowledged was well intentioned but misguided. Beware's Anarky is a self-diagnosed sociopath and aimless terrorist whose only difference between him and The Joker is name and chess theme.
Also from Beware the Batman is Sapphire Stagg, the good-natured love interest of Metamorpho in the comics, who is here depicted as very much similar in nature to her corrupt father, Simon Stagg.
Add Harvey Dent, who is usually a man of justice and a big supporter of Batman (at least before his transformation into Two-Face), now a hater of Batman who teams up with Anarky to kill him and hires Deathstroke to take down Batman, to the list.
Sort of with Ra's Al Ghul. His actual motivations are unclear, but he doesn't seem to have the Well-Intentioned Extremist goals of his comic counterpart. On the other hand, he seems hellbent on focusing on Gotham only, so the rest of the world doesn't have to deal with genocidal plots.
In the book Cranberry Christmas, Cyrus Grape is a curmudgeonly old man who refuses to let anyone skate on his pond, but gets his comeuppance when Mr. Whiskers finds a deed that proves the lake is actually on his property. In the animated special, Cyrus is a much more active antagonist, sneaking around and messing up Mr. Whiskers's house in order to keep Mr. Whiskers from finding that deed (whereas in the book he had no idea it existed).
Transformers Animated actually did this to the character Waspinator from Beast Wars. While Beast Wars Waspinator is portrayed as the lovable Butt Monkey who does nothing but get kicked around by other characters (though he does manage to injure the occasional Maximal, usually not by accident), Animated Waspinator, now renamed Wasp, is downright terrifying, and wants to get revenge on everyone who abused him.
Young Justice: Klarion the Witch Boy, whose portrayal in the comics generally ranges from an annoying troublemaker (Jack Kirby's version) to a well-meaning anti-hero (Grant Morrison's version), is much more solidly on the side of the black hats here.
Also played straight with L-Ron. In the comics, he's a sidekick to the Justice League International, while in the show he's Despero's assistant.
Speaking of Klarion, he's also clearly evil when he appears in Batman: The Animated Series, stealing control of Etrigan from Jason Blood, tearing Gotham apart simply for fun, and using potential lethal spells on Batman when the hero tries to stop him. He finally crosses the Moral Event Horizon by telling Etrigan to kill Blood (who is aging at an accelerated rate and nearly helpless due to the Demon being separated from him).
Tublat the gorilla from Tarzan by Edgar Rice Burroughs. In Disney's The Legend of Tarzan, his character is merged rather confusingly with another, Kerchak. Since Disney decided to make their version of Kerchak (who is ironically more similar to Burroughs's Tublat in personality) more sympathetic, as a consequence they ended up making their version of Tublat more sinister, like the novel's Kerchak.
Similarly, Professor Phineas T. Philander went from Professor Porter's absent minded friend and colleague in the books to his rival and Smug Snake in the animated series.
Ricochet is a member of the Enforcers (Fancy Dan) rather than a teen vigilante like in the comics.
Anubis is a villain in the TV show Mummies Alive!, when he was actually a good god in Egyptian Mythology who guarded and protected the dead. Set is also seen with Anubis, while Set disowned him in the myths for siding with Horus.
Ammit, on the other hand, is portrayed as a pet of the Big Bad. In Egyptian mythology she was a neutral enforcer of order and punisher of evil, although this quality made her feared by the ancient Egyptians.
The Street Fighter animated series made Zangief into one of M. Bison's lackeys, despite the fact that Zangief actually opposed Shadaloo in the games.
Colossus and Gambit were members of Magneto's Acolytes in X-Men: Evolution, despite being actual members of the X-Men in the comics. They eventually pulled a Heel-Face Turn and were seen as part of the team in the epilogue.
For some odd reason, Wolverine and the X-Men is FULL of this (possibly some of these characters would have returned as heroes had the second season been made):
Domino is a member of the X-Force and X-Men in the comics, but is depicted as a terrorist and member of the Brotherhood of Mutants in the show, basically becoming Mystique in all but name and powers as Mystique herself is The Dragon to Magneto.
Multiple Man is a member of Mr. Sinister's Marauders, despite being a main character in X-Factor since the 90's.
Likewise, the Stepford Cuckoos are shown as villainous members of the Hellfire Club, despite being students at the Xavier Institute in the comics.
Psylocke assists the Brotherhood in one episode, but she's shown to be a reluctant recruit who only helps out the group because she owes Quicksilver a favor.
Mercury, another member of the Acolytes, was a member of the New X-Men in the comics.
In the comics, Scarlet Witch and Quicksilver abandoned Magneto very quickly and joined The Avengers. In the show, Quicksilver is still a member of the Brotherhood, while Scarlet Witch is loyal to her dad. It isn't until the finale that she finally realizes what a monster Magneto is and turns against him.
Mags himself: in the comics, he's a Well-Intentioned Extremist or an Anti-Hero depending on the decade. He was last wa-ha-ha evil in The Seventies, and the last time he was an enemy was done in such an Out-of-Character Moment that it was Retconned into being someone else immediately, making a 1993 storyline the last time we saw him as anything but his normal portrayal (half the team wants to trust him, the other half says "yeah, but you don't know how bad he was when he was bad," and his Wild Card moments don't make anybody any more comfortable.) and it's not like nobody provoked him then. WATXM Magneto appears to be similar to comic Magneto at first but at heart is as monstrous as it gets, more like his sixties/Morrison/Ultimate incarnations.
Emma Frost. Like Mags, she used to be one hell of a foe (even being Big Bad of New Mutants for a time) but comic fans know that that was a long time ago, at least in the main Marvel Universe. In this one she's The Mole and still the White Queen of the Hellfire Club. However, in the finale she sacrifices her life to contain the Phoenix.
The Phoenix. This is far from the first adaptation to do so, but it's worth mentioning that in the comics, Jean as Phoenix was good but Anti-Hero-ish, had to resist darker impulses but stayed in control (she was actually Phoenix for quite some time), and even saved the universe. It took the Hellfire Club's interference to cause her to become Dark Phoenix. This version uses The Theme Park Version where the Phoenix is a 100% Bad Thing. Of course, the Hellfire Club was trying to control the Phoenix in this version, but it wasn't quite the same as Jason Wyngarde and Emma Frost putting her under More Than Mind Control and pretty much breaking down her self-control bit by bit until we get a monster.
Morrigan in the Darkstalkers cartoon. In the games, she is just having fun with no regard for the rest of the cast, in the show, she's Pyron's minion. The series finale implies she becomes closer to how she is in the games if a season 2 ever came. Also, Anakaris, Bishamon, and to some extent Demitri were victims of this.
The Falcon and Doc Samson appear as part of Code Red, a team of government-sponsored superheroes who act in opposition to the Avengers. In the comics, the Falcon is Captain America's sidekick and a longtime member of the Avengers himself, while Doc Samson is an ally of the Hulk. Partially justified though, since it turns out they were brainwashed by the Red Skull. (And both of them have had notable Brainwashed and Crazy stories in the comics; in Falcon's case at the hands of the Skull.)
In The Railway Series novels, Diesel only returned to Sodor once in the individual story "Thomas and the Evil Diesel" where he redeemed himself and was given good word to come back. In the Thomas And Friends series, Diesel made recurring returns to Sodor and eventually became a permanent resident, though he ultimately proved as nasty as before, usually acting as the key antagonistic engine and pulling cruel pranks. Similarly to the novel version though, he is given some sympathetic moments.
Reversed for Bulgy, a bus who disliked railways and tried to steal customers from the trains through lying that he accepted rail tickets. In the books, he is punished by being converted into a henhouse. While this is followed in his first appearance in the TV series, he is later repaired, changed into a vegetable stand, and softens towards the other characters.
The animated movie Heidi's Song is a curious example of this, as it not only makes Fräulein Rottenmeier much more villainous and scary, but also turns Sebastian the butler (in the book a Servile Snarker but very much a kind man) into her Dragon — but utterly reverses it when it comes to Tinette the maid, who in the book is a haughty and snooty woman whom Heidi is slightly afraid of but in the movie is a sweet and sympathetic person. Possibly the shift was done so the movie wouldn't have two female villains.
In the Funny Animal adaptation The Legends Of Treasure Island Long John Silver is a more straight up Laughably Evil villain and mostly void of the sympathetic Affably Evil facets of his novel counterpart (and most other variations of). Perhaps most notably, his fatherly role with Jim is completely gone and for the most part, he would love nothing better than to just send the boy down the plank, or worse.
For most of the Super Friends series, Bizarro is depicted as a clear villain who has murderous designs on the super heroes. However, the final season depicts him faithfully from the comics as a well-meaning bumbler.
While the original comic book incarnation of Teenage Mutant Ninja Turtles' Karai has interests that occasionally pit her against the turtles, she is unambiguously their ally. This has changed in the 2003 and 2012 cartoon adaptations, where she has been made into the Shredder's daughter and subordinate. While she will at times fight alongside the turtles, her divided loyalties result in periods where she is wholeheartedly against them.
The 1980s cartoon is notable for being the only version to portray the character of Leatherhead as truly villainous, as opposed toallotherversions where he is an ally of the Turtles, and any time he fights them in those continuities is because of him being either Not Himself or manipulated into doing it by another antagonist.
Irma in the 1987 series is April's dorky, boy crazed friend who worked with the turtles. In the 2012 series, she's actually a Kraang in a customized robotic suit who was The Mole, faking her friendship with April to find the Turtles' lair.
In other continuities, the Rat King was a lonely man who had the ability to control rats and wanted to be left alone. In the 1987 series, he sought to take over the city for his rat friends. 2003's Rat King only attacked the Turtles when they invaded his territory. 2012's Rat King, on the other hand, started out a Smug Snake scientist who faked concern for his colleague getting mutated so that he could create a serum to give him psychic powers. After becoming the Rat King, he sent his rats to attack New York and mind-controlled Splinter to attack the Turtles. Also, despite claiming to share his earlier incarnations' love for rats, he has no qualms with experimenting on them or sacrificing them in a fight.
Hades wasn't the only guy to fall victim to this in Hercules. In the ongoing series, King Midas - of all people - was made into a would-be Evil Overlord. (Albeit not a very good one and one who repents at the end, but still...)
Zig-zagged and parodied in Teen Titans Go! with Terra. The original Teen Titans made her an example of Adaptational Heroism. In the episode "Terra-ized", she has actions similar to her comic book counterpart; and openly tries to seduce Beast Boy in order to get sensitive information on the Titans. Only Robin and Raven suspect her of villainy, while Cyborg and Starfire are not convinced despite Terra trying to bring them down every scene she's in. When Beast Boy tries to return her advances, she drops all pretense and decides to fight the Titans for the information she needs.
Sunset Shimmer counts too. Her toy bio doesn't give any hint she's remotely malicious.
Brainy in The Smurfs episode "King Smurf" became the titular character, whereas in the original comic book version he was a contender for the role of the village leader who was outvoted in favor of the Smurf who would become King Smurf.
In The Little Prince, the yellow snake, while he represents death, is not necessarily a villain, and may even be ultimately helpful. While the narrator sees him as evil, the Little Prince himself does not, and it is left open as a possibility that the snake, by biting him, did help the Prince return to his asteroid. In the animated TV series adaptation, the Snake is an unambiguously evil, even demonic Eldritch Abomination who travels around the galaxy corrupting planets by tempting their rulers to give in to their basest desires.
Alcuard is a mole in Captain N: The Game Master, and ends up turning on the main characters, including Simon Belmont, in favor of his father, Dracula. In the Castlevania video games, Alcuard's firmly on the side of the good guys, hates Dracula, and is one of Simon's main allies in the series.
Tintin: In the comic strip album Cigars of the Pharaoh, when Tintin drives two people to the insane asylum, the evil fakir switches the doctor's letter for a forged one that tells the personnel to lock Tintin up instead. In the Ellipse-Nelvana animated version, the doctor himself is revealed to be one of the masked villain councilmen and is implied to have written the "bad" letter himself.