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In the comics, "Deathlok" referred to multiple characters, all of which were heroes. In the show, "the" Deathlok is a basically good person but Trapped In Villainy. "Ragtag" also reveals that the original Deathlok is also The Clairvoyant, the Season 1 Big Bad.
The Clairvoyant is ultimately revealed to be Agent John Garrett, a loyal S.H.I.E.L.D. agent in the comics. This ties in with Captain America: The Winter Soldier, where some agents who were good in the comics are part of the Hydra infiltration of SHIELD. Just like the heroes themselves, the audience no longer knows who to trust.
The episode "Dodger" turns a Loveable Rogue from the comics into a ruthless and calculating killer.
Eddie Feyers in the comic was a shady character but basically an ally to Green Arrow, as long as his CIA bosses didn't say otherwise. After Ollie's death, he even became a Parental Substitute to Conner Hawke. His live action counterpart is the Big Bad of the Season One island flashbacks.
"Blast Radius" introduces Shrapnel as a Mad Bomber, which is a reasonable depowered version of the character. The adaptational villainy comes in when the group he's part of - which is identified because they regularly use that kind of bomb in their terrorist activities - is called The Movement.
Helena Bertinelli, AKA the Huntress, is also changed from a brutal Anti-Hero (think Batman without any issue with killing) with a strict moral code into an Anti-Villain who carelessly kills innocents to get revenge on her father. She seems to be getting better by the second season, choosing to spare a few people she could have easily killed, though still threatens to kill hostages, and at the end realizes how pointless her revenge scheme was.
Helena's father Frank Bertinelli is also far more villainous; in the comics, Franco Bertinelli was a mobster still, but one who seemed to genuinely love Helena before he was murdered by her biological father, resulting in her becoming Huntress to avenge his, and the rest of her family's deaths. The show however has him as the object of her vendetta, for killing her beloved fiancé, and once he finds out she's trying to kill him he sees no problem in trying to blow her brains out the first chance he gets. Like above, the Second Season has him genuinely remorseful for being the one who turned his daughter like this and willingly accepts the fact she's going to kill him, hoping it'll stop her warpath.
Elementary: Irene Adler doesn't exist, and is a false identity of Jamie Moriarty.
From Dusk Till Dawn: This happens to Carlos. In the original movie he was merely the brothers’ contact in Mexico and unaware of the Titty Twister’s true nature. In the series he’s a full blown vampire.
Littlefinger is a lot less subtle in the series than in the books. The book version makes a game of looking like The Trickster who is snarky but generally harmless. The live-action version is a Devil in Plain Sight who's openly feuding with The Spymaster of the series. Furthermore, in the books, he isn't involved in anything so vile as serving up his prostitutes to necrophiliacs and serial killers.
Doreah does a Face-Heel Turn in the show that was not in the original books. This is probably because she simply dies of illness in the books, so the show gives her a more eventful demise.
The character Dagmer Cleftjaw was written out of whole cloth for the series. In the books, he's an Honorary Uncle for Theon Greyjoy, and sticks up for him. All in all, he's a fairly decent guy, at least by the standardsof theIronborn. In the series, he's an Evil Mentor who seems set to guide Theon to alienate himself from the Northmen he grew up with, corrupting Theon as much as possible, and then sells Theon out when it's a choice between that and dying in a blaze of glory.
In the show, Stannis Baratheon is made more morally grey by being much less concerned about the prospect of sacrificing innocents in magical rituals to secure his throne. He also physically assaults Melisandre at one point.
The show finally managed one that the fans actually liked with Sansa Stark, who becomes a Magnificent Bastard in her own right alongside Littlefinger, and is likely even plotting against him in some way.
Rast is a rapist and a Jerkass in the books too, but he never betrays the Night's Watch, and dies defending Castle Black against wildlings. In the show he stabs Lord Mormont to death himself, and reluctantly sacrifices an infant to the White Walkers before being killed by Ghost.
In the books, Xaro Xhoan Daxos wants nothing more than to marry Dany so he can get control of one of her dragons, but in the show he allies with the warlocks to assassinate the rest of the Thirteen and seize control of the city, then imprison Daenerys and steal all of the dragons.
Joffrey is a horrific power-crazed psychopath in the books, but his show counterpart's taste for sexual violence against prostitutes is an exaggeration (or perhaps an extrapolation, given his age-up) of his sadistic streak. He also treats Cersei far worse, and two of Cersei's biggest Kick the Dog moments in the books are done by him instead.
Jaime gets extra villainous actions than he had in the book, including murdering a member of his house whilst imprisoned by Robb. In Season 4, his sex scene with Cersei is considerably more forceful than that described in the book, causing many viewers to regard it as rape.
In the books, the Thenns are more traditionally civilized than other Wildlings, characterized by their higher technology and greater respect for authority. In the show, they're changed into a group of scarred up, gleefully sadistic cannibals that disgust even the other Wildling raiders.
Justified: Raylan's father, Arlo Givens, is a ruthless Manipulative Bastard and lifelong criminal with few redeeming qualities. In the original books he was a coal miner who died of black lung when Raylan was still a teenager.
Kamen Rider Fourze does this in a couple of its Movies, which adapt characters from other Shotaro Ishinomori shows. In Everyone, it's Space Time!, the villains are based off of the Space Ironmen Kyodain, while in Movie Wars Ultimatum they're based off of the Akumaizer3. For a bonus, the former also inverts this trope by featuring heroic characters based off of Kyodain villains Black Knight and Goblin Queen (though with her it's sneaky; the name Inga Blink is a Significant Anagram in Japanese; the katakana easily rearranges from Inga Burinku to Gaburin Kuin by moving one character from the end to the beginning; we're basically talking Pig Latin.
Lois and Clark: Mr. Mxyzptlk received this treatment. He was a superpowered imp from the 5th dimension like in the comics, but rather than the relatively harmless trickster as he usually is, here he's a Faux Affably Evil villain who traps the world in a time loop where each time around humanity grows more depressed and pessimistic to make them all cross the Despair Event Horizon and destroy themselves.
Once Upon a Time: They did a really big twist by turning Peter Pan and most of the Lost Boys into the villains. Word of God says they decided to do this because they thought about how messed up a person would have to be if they wanted to remain a kid forever. Interestingly enough, Captain Hook, one of the show's villains, is redeeming himself in the third season - the very season where Pan is the Big Bad.
Season 4 turns Little Bo Peep into a villain of the week, making her a witch warlord who turns people into her "sheep" by enslaving them with magic if they can't pay their debts to her.
All twelve of Hans' brothers are minor antagonists, while they were neutral characters in 'Frozen. While the behavior of at least some of them towards Hans contributed to his villainy (according to Word of God), they were never directly antagonistic towards Anna and Elsa, and his scheme took place without their knowledge or approval. In the series, they attack Arendelle under his leadership.
Once Upon a Time in Wonderland turns the Caterpillar into a villain; he was a side character who gave cryptic advice in Alice in Wonderland, but turns out to be more like a mob boss in the series. (Then there's Jafar, who was evil to begin with and got worse.)
Sharpe: The television adaptation of the novel Sharpe's Battle was written before the novel had been finished, resulting in a vastly different second half. So while Lord Kiely gets a much more sympathetic treatment in the adaptation and dies a heroic death (rather than blowing his brains out on realising he's a bit rubbish), Spear Carrier Guardsman O'Rourke, whose main contribution in the novel is to say his name when Sharpe asks him, gets turned into a Turn Coat who kills a couple of likeable characters mostly because they're there.
This happened to Salem in Sabrina the Teenage Witch. When Sabrina first appeared in Archie Comics, Salem was little more than a pet cat who occasionally had human thoughts. The series changed him into a more active character, and made him a once-human warlock who had been transformed into a cat as punishment for attempted world conquest. While not a true villain on the show (most of the time) he's usually the resident Jerkass.
This partially reverses in the animated spinoff. By making the main characters younger (in the case of Sabrina's aunts, not by their choice) while keeping the show's Competence Zone roughly the same (spread wide but leaning towards adulthood), Salem becomes no less snarky but more relatively competent and significant to plot resolution. Switching to animation also gave him a greater range for physical activities, diminishing the need to write him as a bystander. This meant making him either more directly villainous or more helpful - and as he's nominally a (now little) girl's pet, the writers went for the latter.
Sherlock: In the original story Irene Adler has an incriminating picture of herself with the King of Bohemia which she has not intention of using, and keeps as protection against him. In the show she has multiple pictures of various important people she keeps as insurance, but also hands top secret counter-terrorism information to Moriarty, and blackmails the British government with the photos for millions of pounds to satisfy her own power fantasy.
Sleepy Hollow: In The Legend of Sleepy Hollow, Abraham was the local hero who played a prank on Ichabod Crane by pretending to be the Headless Horseman. The show's version of Abraham is the Headless Horseman, with downright murderous intentions for Crane.
This version of Bizarro is less of a Harmless Villain and more of a dangerously intelligent one.
Mr. Mxyzptlk isn't a funny omnipotent imp, but more of a smug psychopath who likes to use his Mind Control to induce Squick and tries to stab Chloe for a deal with Lex Luthor.
Lana Lang is also turned into a much shadier character.
The comic book incarnation of Zor-El sent his daughter, Kara, to Earth as a protector for her cousin, though initially he was wrongly believed to have been a villain who sent his daughter as an assassin. The series made him an outright villain who sent his daughter to Earth as part of a plot to have himself resurrected as a conqueror.
Super Gran: In Forrest Wilson's books, the character Tub, while initially a somewhat reluctant henchman to Campbell, becomes a good guy in later books following a Heel-Face Turn. In the TV show, he is a Card-Carrying Villain who goes along with Campbell's plans unquestioningly.
Stargate SG-1 does this to nearly every polytheistic pantheon, as the Goa'uld are Always Chaotic Evil and named after (or inspired; it's never made clear) most early human religions. The most obvious example is Anubis, the most evil Goa'uld by a huge margin who shares a name with a good god in Egyptian Mythology.
The real villain isn't the Affably Evil Silver; it's Squire Trelawney, who plots to cheat Jim and Dr Livesey out of their share of the treasure, arranges for Mrs. Hawkins to be thrown out of the inn while they're away, has Mr. Arrow executed, and eventually suffers a Karmic Death by diving after the treasure when Jim throws it overboard. Not much like the excitable but well-meaning "most liberal of men" in the book.
Tom Redruth, Trelawney's gamekeeper, gets this, too - in the book, he is an elderly man who accompanies Trelawney to the island and is killed by the mutineers. In the series, he is Trelawney's vicious enforcer back in England.