Shere Khan himself is upgraded slightly with each Disney adaptation. In the books he was an antagonist, but represented as somewhat pitiful (he has a bad leg, restricting his ability to hunt), is something of an arrogant fool, and is taken half-heartedly by a lot of residents of the jungle, including Bagheera. The other animals generally see him as a troublemaker and a coward because he attacks humans, and characters like Bagheera and Kaa command a lot more respect and fear. 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 TaleSpin, 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.
The Phantom Tollbooth: the Lethargians in the book are merely unhelpful small creatures and suggest that Milo rest and not go anywhere - frankly, they were too lethargic to do anything so difficult as trying to stop him physically. The movie Lethargians can liquefy their bodies, and then combine or separate from one another, and use the suggestion of rest only as a ruse, to allow them to either kill Milo or make him one of them. After all, breathing is doing something.
The Rats of NIMH:
Jenner in the Don Bluth film The Secret Of NIMH, what with destroying Mrs. Brisby's home and killing Nicodemus. However, in the book the film is based on, he is not nearly as villainous, but is a slightly more sympathetic and much less malicious Commander Contrarian who only appears through flashbacks and dies offstage. He disagrees with Nicodemus about leaving for Thorn Valley, but he doesn't resort to violence like his film counterpart.
In the movie, Brutus, while he isn't a villain, scares Mrs. Brisby away from the rosebush while in the book he just gives her a hard time about it before he ultimately lets her in. The book also makes it more clear that it's just an act and Brutus isn't really mean, although he does try and help pull up the Brisby home later in the film, too.
The human scientists at NIMH in the book are portrayed as simply people doing their jobs - they are not pointlessly cruel to their research animals and even treat them kindly. In the film, they are mad scientists who abuse the animals and the reasons for their experiments aren't explained.
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 the Disney movie Bambi, Ronno the deer is a jealous bully who spends much of his time antagonizing Bambi, culminating in their battle over Faline. In the original book, Ronno and Bambi were actually good friends instead of enemies, although this does change as they grow older and see each other as competition for does.
The human hunters in the book are ordinary people who are frightening and god-like from the perspective of the animals, although Bambi's father makes a point of showing Bambi a dead hunter to teach him that humans are subject to the same rules as the forest animals are. In the Disney movie, the hunters are explicitly reckless and careless, shooting everything that moves and setting the forest ablaze from a badly tended campfire. Bambi's mother is, judging from the time of her death in early spring, the victim of a poacher.
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.
The Sea Witch in the Hans Christian Andersen fairy tale is a 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 film The Little Mermaid, 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.
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.
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.
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.
Frollo was originally archdeacon of Notre Dame; in the movie, the archdeacon is a seperate, kindly character, who induces a guilt trip on Frollo at the beginning and is beaten up by him at the end. In a sense, both these scenes depict the man struggling with himself. It's believed the reason for this Adaptational Villainy was due to Disney being concerned that having a priest for a Big Bad would offend people, and their solution was to divide the literary character in two and give one all the good qualities and the other all the bad.
The Queen of Hearts is depicted as an Ax-Crazy villainess in the Disney adaptation. 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.
The King himself goes from pardoning people to openly supporting the Queen's executions.
The White Rabbit in the Disney version is a pompous servant of the Queen. In the book he's a little friendlier to Alice, advising her not to play well in the croquet game so the Queen can win.
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 books, they are fairly explicitly the actual Fates. (Taran's mentor Dalben was originally raised by them, which is why he's so weird.)
In 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.
Pentstemmon was Howell's beloved mentor. Suliman marries Sophie's sister.
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 first live-action Street Fighter movie and Street Fighter American cartoon. This makes his comments toward Ralph during his sole scene all the more poignant.
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 (although, incidentally, the scene mentioned above still happens anyways).
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 not as brave or capable as Tarzan, and his worst crime is concealing Tarzan's true identity after he figures out the truth so that he can keep the title. Other than that, he is a decent man who is willing to sacrifice himself for Jane. In the movie, he is an Egomaniac Hunter.
The Kralahome in the animated version of The King and I is not a stern but genuinely loyal chancellor, but rather an Evil Sorcerer who actively plots to overthrow the King.
Romeo & Juliet: Sealed with a Kiss is a loose and Lighter and Softer adaptation of William Shakespeare's Romeo and Juliet with most of the characters depicted as seals. The villain is an elephant seal named Prince, a Composite Character of Prince Escalus and Paris, a member of his family who is arranged to marry Juliet. The Prince in the play is a Reasonable Authority Figure whose antagonism comes from his frustration with Romeo and Juliet's Feuding Families, while Prince in the film is a Fat Idiot villain who banishes Romeo to a shark-infested island out of jealousy. While Romeo was banished in the play, this was an act of mercy on the Prince's part as the alternative was Romeo being outright executed for murder. Paris, although his exact characterization depends on the production, seems to genuinely care about Juliet, courts her in the appropriate manner for the time period by asking her father, and is at worst a Type IVAnti-Villain who attacks Romeo because he thinks that Romeo is vandalizing her tomb.
Whereas in the comics, Algrim/Kurse was loyal to Asgard after he cut ties with Malekith, in Thor: Tales of Asgard, Algrim's presented as resenting Odin and Asgard for not coming to the aid of the Dark Elves against the Ice Giants (and going against them when the Dark Elves turned to Surtur for help) and blames them for the extinction of the Dark Elves, and was willing to use the Sword of Surtur against Asgard.
Justice League: Gods And Monstersnote Designed as an alternate universe to begin with, so these are far from the only changes to mainstream versions. Batman usually isn't a vampiric Kirk Langstrom, for example.:
In the movie proper, Doc Magnus and the Metal Men are the main villains.
Also from the movie proper, Highfather is willing to double cross Darkseid.
The tie-in miniseries, Justice League: Gods and Monsters Chronicles sees Harley Quinn undergo this. Sometimes, Harley is portrayed as an Anti-Villain with some sympathetic qualities. This version, however, is an Ax-Crazy psychopath who would hurt a child—and as the Joker isn't seen, this version is doing this of her own free will.
In The True Meaning of Smekday, the Gorg were the true Big Bad while Smek was more incompetent than actively malevolent. In Home, he's the Big Bad, and the Gorg are only attacking the Boov because he stole a rock containing the next generation of the Gorg species.
The titular Batwoman in Batman: Mystery of the Batwoman is much more of an anti-heroine than the original Kathy Kane (and it predated the Kate Kane Batwoman), so they DC insisted that the filmmakers not actually use Kathy Kane. This didn't stop them from homaging her via the character Kathy Duquesne or making her a suspect... or even making this Kathy one of the Batwomen.
In Dinotopia: Quest for the Ruby Sunstone, Ogthar is the main villain who plots to conquer Dinotopia. In the original books, King Ogthar was a mythical king who is spoken of by dinosaurs and humans alike with great reverence.