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.
Played with in the case of the Greek gods and goddesses in Wonder Woman. 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.
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.
Chaos in Sonic the Comic, 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 (see below), then he becomes even worse than his game and other incarnations by trying to destroy Mobius outright.
Even Sonic himself to an extent, who is a much bigger Jerkass. Also Super Sonic is a psychopath.
The New 52 version of 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.
The antivillain version of Freeze was based off of Batman: The Animated Series. The original Freeze, from the Silver Age, lacked any humanistic 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 New Genesis 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 Other", 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.
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.
Transformers: Last Stand of the Wreckers: Overlord's appearance 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, but that pales in comparison to his appearance in LSTOTW (and later MTMTE), where he is one of the most depraved Decepticons ever, murdering populations of creatures, pitting Autobot prisoners against each other and his own troops for his amusement, and then executing all of them so they can't be rescued.
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.