One of the most famous examples is Kaa. In the book, he is a mentor and friend of Mowgli, helping to save him when he is kidnapped by monkeys and offering him advice for battle against the dholes, indeed never harming or threatening him in any way. The other animals in the jungle respect and fear him for his wisdom and powers of hypnosis, which only Mowgli, because he is human, is immune to. In the Disney movie and its sequel, he is a cowardly, greedy villain who only sees Mowgli as potential food and is also a pathetic Butt Monkey. Apparently it was thought by Disney that audiences wouldn't accept a snake as a heroic character. In the sequel Kaa, while still a conniving predator, is rather ineffective and pitiful (well, he was pretty pathetic from the start, but the sequel takes it up to eleven). The live-action movie adaptation portrayed him as a mindless monster who is used as a Shark Pool by King Louie against thieves (in the novel, incidentally, Kaa was the only animal that the monkeys were afraid of); this depiction draws on a different snake who appeared in The Second Jungle Book.
Shere Khan himself is upgraded slightly with each Disney adaptation. In the books he was an antagonist, but represented as somewhat pitiful, is something of an arrogant fool, and is taken half-heartedly by a lot of residents of the jungle, including Bagheera. In the original Disney film, he is somewhat comedic and playful, but is genuinely feared and implied to be stronger than many animals put together. In Tale Spin, he is given a much more deathly serious and calculating demeanor, but also is rather affable and more of an Anti-Villain in many of his appearances, with a moral code that restrains his villainy. In the sequel to Disney's Jungle Book he is an out and out dark presence whose only goal is to rip Mowgli to shreds.
Interestingly the Jungle Cubs animated series refers closer to both characters' novel personas. Kaa is a friend of the other animals and, while still a predator, is far less intentionally antagonistic about it than his adult counterpart. Meanwhile, Shere Khan is an arrogant bully, but somewhat ineffective and occasionally sympathetic. In a chronological sense, this means the Disney counterparts started off loyal to the novel ones, before being embittered into their more malicious adult forms.
In the (non-Bluth directed) sequel to the movie, Martin, a good guy in both the film and book, becomes a crazed villain (although as the result of brainwashing).
Ivan Sakharine in the Tintin comic The Secret of the Unicorn. While sinister-seeming and a nuisance, he isn't evil, and is victimized by the real villains, a pair of unscrupulous treasure hunters. He even gets an implied Pet the Dog moment - a cameo in Red Rackham's Treasure suggests that he offered his own Unicorn model for Captain Haddock's maritime gallery, and in turn Haddock seems to be on good enough terms with Sakharine to invite him to an exhibition there. In the movie based on the same comic, he is a much darker and more threatening character with a blood vendetta against Haddock's family who takes over the role of the comic's villains.
In Disney's Hercules, Hades is a Satan-like villain (again), intent on overthrowing Zeus and taking over Mount Olympus. In Greek Mythology, he was a neutral but just ruler of the dead and no worse than the other Greek gods. Hades had no antagonism towards Heracles, only meeting the hero when Heracles asked to borrow Cerberus for one of his twelve labors. Heracles's original divine enemy was Hera, his stepmother and Zeus's wife. As for overthrowing Zeus, Hades never tried that in the myths. While Hades did kidnap Persephone (with Zeus's permission), he was nowhere near as bad a husband as his brothers Zeus and Poseidon.
In fact, Hades is probably the least antagonistic god Hercules ever met in the original myth; the entire obstacle Hercules has in borrowing Cerberus is that Hades politely asks Hercules to bring it back when he's done.
Face it, the movie (and the series that came after) has very little resemblence to actual mythology at all. Hades once claimed that he was Poseidon's "baby brother" in one episode of the show. Any student of mythology knows that he was the eldest brother.
The Sea Witch in the Hans Christian Andersen fairy tale The Little Mermaid is a True Neutral character who shows no vindictive intentions toward the unnamed mermaid, only making the famous tongue-for-legs exchange, even warning the mermaid of the consequences of the transformation. She doesn't go back on the deal or interfere with her relationship with the prince until she is asked to by the mermaid's sisters, and only indirectly. In the Disney Animated Canon, she is named Ursula, is an out-and-out villain with a tendency toward Faustian deals, and gets in the way of Ariel's romance with Prince Eric far more than the character in the fairy tale did.
Ursula also takes the place of the princess who the prince eventually marries in the original, who is innocent in Andersen's fairy tale and genuinely loves him.
The witch being evil in Disney's version may have been pinched from Dvorak's opera Rusalka; both it and Andersen's story are themselves adaptations of a medieval French fairy tale.
It may be surprising to learn that Claude Frollo of The Hunchback of Notre Dame was a more sympathetic character in the original novel by Victor Hugo. While driven to evil deeds later by his lust for Esmeralda, he willingly adopts and cares for Quasimodo, instead of threatening to throw him down a well as he did in the Disney version of the story. All while looking after his layabout of a brother, Jehan (who most movie adaptations composite with Claude), and being orphaned himself to boot. He was also more tolerant of gypsies, asking only that they keep their activities away from the cathedral rather than actively hunting them down.
The Queen of Hearts is depicted as an Axe Crazy villainess in the Disney and Tim Burton adaptations of Alice in Wonderland. In the book by Lewis Carroll, while she does constantly order executions, the King quietly pardons everybody she sentences to death when she isn't looking and no real harm is done. She never notices this, and the inhabitants of Wonderland just choose to play along with her. Also, it's outright said by the Gryphon that she doesn't execute anyone.
In the children's book The Brave Little Toaster, the new appliances in Rob's apartment are friendly and helpful to Toaster and the other older appliances, helping them find a new owner via a radio show, and feel guilty for their role in replacing still useful appliances. In the movie, they are arrogant and cruel to them, even tossing them into a dumpster out of jealousy.
The three witches in The Black Cauldron are grasping and sneaky, if not evil, characters who try and trick Taran into giving up a treasure for the cauldron. In the book, they are neutral figures who bend their own rules to help Taran and the others get rid of it.
In the movie adaptation of Howl's Moving Castle, the main villain of the book, the Witch of the Waste, is downgraded and drained of power. Meanwhile, two of the book's nice characters, the kindly, motherly Mrs. Pentstemmon (who in the book is murdered by the Witch) and the absent and also kindly Wizard Suliman (who in the book is captured and cursed by the Witch) are combined into one character and made evil, the real villain of the movie.
Inverted in Rock-A-Doodle with Snipes the magpie. In Chanticleer, the play which the movie is loosely based on, the Blackbird is a villainous character who plots to kill Chanticleer. In the movie, his counterpart Snipes is a Jerkass, but is also one of Chanticleer's allies and nowhere near as bad as the Blackbird in the play.
In Wreck-It Ralph, a number of villains get together for a support group, and among them is Zangief, who isn't a villain in the games. Though he is often a victim of this trope, being a villain in both the Street Fighter movie and Street Fighter cartoon.
The puppeteer from Pinocchio (Mangiafuoco in the book, Stromboli in the film). In the film he was far more cruel and simply wanted to exploit Pinocchio and states that he'll use him as firewood after he can't perform anymore. In the book although he initially does want to use Pinocchio as firewood after the boy accidentally ruins one of his puppet shows, Pinocchio is able to convince him not to do so, and he even gives the talking puppet some coins to help Geppetto out.
This is probably an influence from Alexey N. Tolstoy's book adaptation, Buratino, where the puppeteer, named Carabas Barabas, is the main villain and a very ominous person.
Clayton in Disney's Tarzan. In the novels, he is Tarzan's cousin who inherits the title after Tarzan's parents are presumed dead. His worst fault is that he is a coward, and his worst crime is concealing Tarzan's true identity after he figures out the truth so that he can keep the title. In the movie, he is an Egomaniac Hunter.