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.
Herakles in the modern adaptation is portrayed as a villain who raped Hipoolyta (instead of just seducing her). He becomes The Atoner, however.
This also happens to the the Hulk, Hank Pym, several X-Men, and the Black Widow, who become more villainous characters in the Ultimate Universe than their original incarnations were.
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 the Ultimate Universe.
John Rockerduck is portrayed as a Corrupt Corporate Executive in several stories but he was by no means this or any other kind of villain in the only story his creator used him.
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 Sonic Underground 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 Silver Banshee is an inversion. Pre-reboot she was an out and out villainess but the new version has been introduced as a very sympathetic character who seems set to be an outright heroine or at worst a Tragic Villain. Being Supergirl's only friend and having a supervillain father complicate things.
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.
Spike Witwicky in the IDW 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 predating that was his appearance in LSTOTW. In Wreckers 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.
