In general, spies, whether good or bad, are regarded as inherently shifty characters with M, the leader of M16 and the creator of the league, revealed in Volume 1 to be James Moriarty and his successor, the nominally good Mycroft Holmes shown to be if possible, more ruthless. The Black Dossier takes this even further with a very negative portrayal of Cold War era spy fiction, M16 pulling The Coup and installing Big Brother from Nineteen Eighty-Four and being led by Harry Lime with characters like Emma Peel shown as little more than an Unwitting Pawn and James Bond a misogynist scumbag who is a traitor to England and working for the CIA and becomes a Karma HoudiniVillain with Good Publicity.
Providence averts this in general for most of the Lovecraft characters in the story. It makes an exception however for Ronald Pitman, the Captain Ersatz of Pickman from Pickman's Model. Nothing in the original story suggests as Moore's comic does, that Pitman is a Serial Killer and Mad Artist.
In the The Mighty Thor comics, Loki is generally depicted as an evil god (though some individual writers have made him more of an Anti-Villain), but in the original Norse mythology he's a much more ambiguous figure, usually taking the role of The Trickster.
He himself noticed this and killed himself in the Siege to change. His success is... ambiguous, but he managed to not go back to straight up villainy for years until 2016 where he joined a team of Asgardian villains.
Played with in the case of the Greek gods and goddesses in the comic. A number of them started out as Lighter and Softer than they were in Greek Mythology. However, Ares, the God of War, is portrayed as so dangerous and Too Powerful to Live that Wonder Woman has to actually kill him in at least one adaptation. Ares in the Greek myths, although The Berserker and ironically a bit of a Dirty Coward, looked after his kids and was worshipped like the other gods. However, the more recent Wonder Woman stories have taken to portraying the pantheon as somewhere closer to what they were like in mythology.
The residents of Themyscira has always had its share of misandrists and Straw Feminists, but their attitude had gradually descended over the years from an isolationist community who just wanted to keep men away, to man-hates with a few bad apples, to having a legit excuse for hating men (being the spirits of women who were murdered by abusive spouses), to the New 52, where they have truly become evil, seducing and murdering men in order to reproduce and engaging in child slave trading. not all fans were pleased. The New 52 explanation has been retconned away with DC Rebirth by revealing that everything Diana knew of them was actually a lie.
Heracles in the modern adaptation is portrayed as a villain who raped Hippolyta (instead of just seducing her). He becomes The Atoner, however.
Ironically, in the New 52 Wonder Woman series, Ares (only referred to as "War") is one of the few Olympians who isn't somewhat villainous. The most villainous of the Olympians is Apollo, one of the most noble Olympian gods in the original mythology.
Cottus, one of the Hekatonkheires, is a major enemy of Wonder Woman and a frighteningly powerful Person of Mass Destruction. In mythology, he and his brothers allied with the Olympians against the Titans and he was their jailer in Tartarus.
Black Widow is basically a reversal of her original counterpart, who started off as an evil Russian spy before reforming and becoming an Avenger. Here, she's introduced as a seemingly heroic defender of justice, but turns out to be a murderous traitor acting as The Mole for the Liberators.
Also, Jean DeWolf, a heroic female police officer in the original Spider-Man comics, was made a corrupt double-agent working for the Kingpin in Ultimate Spider-Man. Iron Fist also worked for the Kingpin, albeit he was blackmailed into it.
Nick Fury is self-serving and corrupt, willing to violate the Constitution and throw people under the bus to maintain his power.
Wolverine, rather than an Anti-Hero who follows a strict code, starts out as an amoral mercenary who literally only joins the team so he can sleep with Jean Grey, and murders people for personal convenience rather than in self-defence or a sense of justice. He gets better.
Similar to her Ultimate incarnation above, the Marvel 1602 version of Black Widow, turns out to be a reversal of her original counterpart, only in this case, she's a double agent for Count Otto von Doom.
There's also the 1602 version of Bruce Banner, who's presented as an Evil Chancellor with Undying Loyalty towards King James I and willingly assists in his goal of arresting Nick Fury and the "witchbreed" mutants for "treason." However, at the climax, he does risk his life to save Peter Parquaugh in a similar fashion to the way he became the Hulk in the original comics by saving Rick Jones.
Chaos, who is depicted as a transformed and already villainous Drakon Prosecutor with no sympathetic backstory or clear motivation. In Sonic Adventure, he is a mutated Chao who was previously peaceful, only turning violent when all of his Chao friends were massacred by the Knuckles Tribe, under the leadership of Chief Pachacamac. Tikal the Echidna, who Chaos tortures in the comic, was his friend in the game, and the two leave in peace after Chaos is calmed down.
Robotnik himself, while still maintaining some of his comical pathos from the games and other incarnations, is far more evil and void of redeeming aspects, gaining a similar dictator role as his Sonic SatAM and Underground counterpart, then he becomes even worse than his game and other incarnations by trying to destroy Mobius outright.
Mr. Freeze, who has been revised to be less of an Anti-Villain. He's still out to cure his frozen wife Nora - but this is a lie. Nora was preserved long before Freeze was even born, he's just deluded himself into believing they're married as part of his obsession with cold. Of course, the antivillain version of Freeze in the first place was based off of his alternate portrayal in Batman: The Animated Series. The original Freeze, from the Silver Age, lacked any such humanizing qualities, being an unrepentant villain who uses a cold theme.
In the original Batman comics, Francine Langstrom was the long-suffering wife of Kirk Langstrom/Man-Bat, whose occasional bouts of being She-Bat were either against her will or out of a desire to keep her family together, and she generally had more control than Kirk did. The New 52 version is an industrial spy who only married Kirk to steal the Man-Bat formula, and who based her own version of the serum on a vampire bat, making her much more vicious than Kirk is..
In the New 52 Teen Titans, Raven is a willing servant of her father, the demon Trigon, and is using the Titans as part of a thus-far undisclosed plan; Superboy is a living weapon who doesn't really "get" morality (and was later replaced by a full-blown murderous psychopath); Cassie/Wonder Girl is a thrill-seeking cat burglar; and Bart/Kid Flash is a former terrorist leader (albeit against a really horrible-seeming regime). Tim/Red Robin is a bit of a jerk as well.
In the original New Gods, the good gods of New Genesis were the creative free-will of chaos, and the evil gods of Apokolips were the stifling controlling forces of order. In the New 52 version (as seen in Infinity Man and the Forever People and Green Lantern: Godhead) they both represent order and control, with Highfather as a Well-Intentioned Extremist, who may be just as much a threat to humanity as Darkseid.
Geppetto and Goldilocks in Fables. In their respective stories, Geppetto is a benevolent, fatherly figure while Goldilocks is nothing more than a harmless, if annoying, intruder. In the comics, on the other hand:
Gepetto is "The Adversary", the vicious tyrant who has crushed thousands of fantasy worlds and murdered billions, all in the name of peace.
Goldilocks is a vicious rabble-rousing anarchist who stirs up revolution just for the fun of seeing people fighting.
Hansel, one of the protagonists of his fairy tale, grows up to become a sadistic witch-hunter and Fantastic Racist who, among other heinous acts, murders his own sister.
In Snow White's backstory, the seven dwarfs were abusers and rapists who treated her like a slave.
Dorothy Gale appears in the spin-off Cinderella: Fables Are Forever and is portrayed as a Psycho for Hire who considers her old friends expendable.
Spike Witwicky in The Transformers is nothing like his G1 cartoon predecessor. While in the G1 cartoon, he is undoubtedly a good guy and aids the Autobots, in the comic, he is an utter jerk to many and has a more sinister, hidden goal for aiding the Autobots.
Overlord in Masterforce had him as a Proud Warrior Race Guy, and honorable enough to turn on his evil boss and help the heroes. His appearance in the Classics community had him as a straight up villain, and Decepticon conqueror. All of them pale in comparison to his appearance in The Transformers: Last Stand of the Wreckers (and later More Than Meets The Eye), where he is the Big Bad, and one of the most depraved Decepticons ever. He murders populations of creatures, pits Autobot prisoners against each other and his own troops for his amusement, and then executes all of them so they can't be rescued.
The Transformers: More Than Meets the Eye does this to Star Saber. In the Victory cartoon, he is a squeaky-clean hero a la Optimus Prime. The IDW comic turns him into a religious fanatic who once called for an atheist Holocaust. He works for the Big Bad to bring about the end of all artificially-built Transformers, including his Good Counterpart, Dai Atlas, whom he had religious disagreements with. This is a carry-over from the author's days in the Transformers UK fandom, where his stories portrayed Star Saber as a fascist.
The Transformers: Punishment gave this treatment to Sandstorm. In the cartoon Sandstorm was a pacifist who's planet was dragged into the conflict. He was quick to befriend people and even palled around with the Decepticon traitor Octane for a time. Most comics place him as a member of the Wreckers, a crack team of Autobot elite soldiers; not a pacifist anymore but not a full on villain. In Punishment he's the Big Bad of the story; having finally snapped in the post war peace he becomes a serial killer hunting down Autobots and Decepticons accused of war crimes, including the Dinobots, and burning them to death.
Baron Karza in the Marvel Micronauts comic books is the Big Bad of the "Homeworld" sector of Microverse. The toy line gave little to no characterization of the various figures. In the toyline, he was described as the rival to Force Commander but he was also one of a number of assorted Magno figures of a similar theme. There were also other European release only characters such as Green Baron and King Atlas. All of these characters were lesser nobles under a figure named Red Falcon who was the right hand of an Emperor Megas. In the toyline, Karza seemed to be evil by default because of color coding and because Karza bore a passing resemblance to another armored villain froma then recent very popularspace fantasy movie. But we don't know for sure if he was the worst of the worst, especially since Megas does an even better job at the passing resemblance.
Wonder Dog in Superfriends is a cute, Scooby-Doo-like mascot. Wonder Dog in the DC comics is a hellhound who disguised himself as a normal dog, killed Marvin, and paralyzed Wendy. He ended up getting killed by the Teen Titans in the end.
In his cameo in the Justice League episode "Ultimatum" he's portrayed similarly as a beast.
In Spider-Man: Noir, Curt Connors is a Nazi-sympathetic scientist and assistant to Doctor Octopus who remorselessly experiments on humans, very different from his mainstream comics counterpart, who is generally a good guy when he isn't having Superpowered Evil Side issues.
In Threeboot Legion Of Superheroes, White Witch, Polar Boy and Chlorophyll Kid (as Plant Lad) are all members of the Wanderers, which is an antihero version of the Legion of Super-Villains, a bit like the Light Speed Vanguard in the cartoon. In the original continuity, White Witch is a Legionnaire, and Polar Boy and Chlorophyll Kid are founders of the Legion of Substitute Heroes.
In Noob, the comic version of Donteuil in regards to the webseries one. When that fact that Fantöm's avatar was illegally enhanced gets revealed in the webseries, Judge Dead is the one who decides to blame the whole thing on its Locked Out of the Loop victim. A couple of webseries scenes give the impression that Donteuil has a My God, What Have I Done? feeling towards the victim in question and it's via Donteuil that the audience eventually finds out that the victim's situation isn't as bad as it first looked. In the comic, Donteuil seems to be the one who decided to pull the "blame the victim" move, while the "situation not as bad as it first looked" reveal comes from a Fictional Document that gets no mention in the webseries, provided by someone else than Donteuil.
The Greater-Scope Villain in Nextwave is Devil Dinosaur. Usually a heroic character, he's now an Omnicidal Maniac in charge of a massive terrorist organization, killed and ate his partner Moon Boy (who is also abusive here), and he can alsospeak. When the events of Nextwave became part of mainstream Marvel continuity, they were both naturally revealed to be evil clones. All Played for Laughs, of course.
Supergirl: Supergirl's father Zor-El was a decent, nice person and a good father in the original pre-Crisis and post-Crisis continuity. In the New 52 universe and Supergirl (Rebirth) he took part in the creation of world-killing biological weapons and became the villainous Cyborg Superman.
Jem and the Holograms: Zig-zagged with Clash. She outright tries to murder Jem (or at least seriously hurt her). In the cartoon she never did anything besides try and get her band embarrassed or make them fail. Even The Misfits don't want to discuss what Clash did. However, outside of that, she's not violent or any meaner than usual.
Laff-A-Lympics: Dread Baron was already a villain in the cartoon but he never tried to double-cross any of his own teammates there. In "The Meet at Mount Ono", when he finds out the Laff-a-Lympic officials placed a chest full of money at the top of the titular mount to be shared among the members of the team that wins the climbing contest, he tries to take the money for himself and isn't above endangering the life of the Rotten athlete originally chosen to represent his team during the contest.
Many of the Marvel characters unambiguously on the side of good that were featured in Ruins who weren'tkilled by the accidents that gave them their powers are portrayed in a far more sinister light, the most jarring examples including Professor X being a corrupt President of the United States who imprisons and mutilates mutants rather than the benevolent leader of the X-Men and Captain America's ally Nomad being a Nazi sympathizer.
In The Flash (Rebirth), Professor Zoom is delighted to learn that one of the differences between the history of this Flash and the one he's familiar with is that Barry's future children, Don and Dawn, become villains because he was never there for them. In the previous continuity, they were the heroic Tornado Twins.
In The Dark Tower novels, John Farson is an ambiguous figure who never appears on the page. He's responsible for the destruction of Gilead... but his numerous followers call him The Good Man, and for all we know he may have had legitimate grievances with the gunslingers. In the comics, we actually get to see him, and he's a psychopathic tyrant who decapitates prisoners to play baseball with their heads.
Cable and Manhunter are both heroes in their respective universes, but become the villainous mercenary Wired.
Deathlok (a cyborg who, in every iteration, wishes to break free of his killing machine programming) and Jason Todd (the then-thought-dead Robin, whose Red Hood Anti-Villain days wouldn't be for another nine years) are merged into a ruthless cyborg HYDRA agent.
Mr. Freeze lacks the redeeming qualities he has in the comics, due to being merged with Nazi scientist Wolfgang von Strucker.
The basic theme of The Wild Storm: Michael Cray is Cray hunting down the Wild Storm universe counterparts of the Justice League, who are all complete monsters.