In the book 2001: A Space Odyssey by Arthur C. Clarke, HAL-9000 is a beautifully-defined and deeply sympathetic character who is so human that he develops a psychosis. The movie, deprived of the ability to use a narrative voice to make this clear, makes HAL seem far more monstrous than the original intent, and sadly the film is often cited as an example of A.I. Is a Crapshoot. The movie of 2010: The Year We Make Contact sticks more closely to the book and redeems HAL, but it's often regarded as a very poor relation to the original movie.
Pius Thicknesse of the books is weak-willed and not the sharpest knife in the drawer, but isn't a villain until he is Brainwashed into becoming one by Voldemort's minions through the Imperius Curse. He's presumably returned to normal after the war, although this isn't shown. In the film series, he is implied to have joined the Death Eaters of his own free will, as he doesn't display traits of characters under the Imperius Curse in the films and is more self-aware.
Grindelwald, while being a villain in both the books and the films, refuses to help Voldemort find the Elder Wand in the book and is killed for it, and it is implied that he feels remorse for his deeds. In the film he outright tells Voldemort where to find the wand.
Hades in the Percy Jackson and the Olympians series is imposing and menacing, described as resembling every dictator in human history, but it turns out that he isn't one of the bad guys, and he eventually helps fight against the Titans while his son Nico becomes an important ally of the protagonists. Not so much in the movie. Whilst merely Chaotic Neutral, his actions in the film make him come off as much less sympathetic (kidnapping Percy's mother to get Percy to hand the Lightning Bolt over to him)than in the book.
Inverted in Street Fighter, where Balrog is a hero and a friend of Chun Li and E. Honda. Played straight with Dee-Jay and Zangief, who were portrayed as lackeys of M. Bison (although the former is Only in It for the Money and the latter does a Heel-Face Turn at the end).
In the short story that It's a Wonderful Life is based on, "The Greatest Gift", Mr. Potter is only the owner of a photography studio and doesn't meet, much less cause problems for, George Bailey. In the movie, he is a corrupt slumlord, Jerkass, and all-around nasty piece of work who goes out of his way to make George's life a living hell (and almost drives him to suicide).
In Jurassic Park, Gennaro the lawyer, while a bit of a Jerkass, is reasonably brave; he went on to punch out a Velociraptor and become The Lancer to Alan Grant (and survives), while fat Dennis Nedry was a programmer who got shortchanged by Hammond, which gives Nedry a more understandable, if not sympathetic, reason to betray him. In the film, Gennaro is a Dirty Coward who got eaten by a T-Rex while sitting on a toilet, and Dennis is essentially an unscrupulous backstabber who is open to bribes.
The movie version of Gennaro inherited all his worst traits (including his depraved cowardice and his violent death) from the character Regis, who appeared in the novel but not the movie. So he's actually a twofer—Adaptational Villainy combined with Composite Character.
Hammond is an inversion. The movie version is a relatively decent man, while novel Hammond is more of a Jerkass (the above mentioned shortchanging of Nedry being one example of his jerkassery) with traits of Never My Fault, blaming everyone but himself (even his grandchildren) for everything going wrong in the end. Movie Hammond lives in the end, while novel Hammond suffers a Karmic Death when he is slowly devoured by a pack of Compies.
In the film version of Last of the Mohicans, Duncan Heyward, although he has a Heroic Sacrifice, is significantly more of a jerk than the character in the book, who not only survives the book, but his descendants remain loyal to Hawkeye.
Faramir, although on the good side in both, is more antagonistic towards the hobbits in the film version of The Two Towers than he was in the book. He also falls under the Ring's spell in the movie - in the book, he's Genre Savvy enough to know that anything made by Sauron is probably dangerous. Word of God says it was because they didn't have enough time to do the complex character development that that scene would require to justify Faramir not trying to take the ring. And yet they took their sweet time to magnify his daddy issues.
Jim Phelps in the first Mission: Impossible movie. In the original series, he was a major protagonist. It seems almost like a deconstruction of what the movie thinks is the 'idea' of Jim Phelps. He's a Cold War agent who ran his own show, but when the conflict is over he finds himself in a low-paying job without a say in policy and a lousy marriage to a woman he doesn't love, so he throws his morals out the window by selling out his country to work for money. Ethan Hunt works as a reconstructed successor to the antiquated "old spy" Jim Phelps, reaffirming his loyalty to his country after they turn on him and ushering in a new era of espionage.
Sentinel Prime, in his earliest appearances in the Transformers comics, was Optimus Prime's predecessor as Autobot leader, and is usually depicted as a good guy. In Transformers: Dark Of The Moon, however, he is the Big Bad and has no qualms about killing and enslaving humans to restore Cybertron.
In the famous movie Dracula (1931), and many other adaptations after it, Renfield is a willing slave to Dracula. In the original book, while Renfield is under Dracula's control, he isn't so happy about it. He even tries to kill Dracula at one point, although unsuccessfully.
A more mild example is that of pre-vampire Lucy. In the book, she's a borderline Purity Sue. In various adaptations she's portrayed as anything from a Femme Fatale to The Vamp (no pun intended) thus introducing a rather unfortunate Madonna/Whore comparison between herself and Mina, with Lucy as the silly flirt who "deserves" to be vamped and staked.
In the film adaptation of How the Grinch Stole Christmas!, the Whos are for the most part more materialistic and unsympathetic than they were in the book, in part to make the Grinch more sympathetic.
October Sky turns Homer's father into a Jerkass, presumably because there wouldn't really be a villain otherwise. In the book it was based on, his father is much nicer and more supportive of his rocketry work.
Also inverted in Silent Hill where Dahlia Gillespie, who was one of the major villains in the first game, but in the first movie she was just a member of the religious cult led by Christabella. Also, unlike Dahlia in the original game, she genuinely loved Alessa and felt guilty for her suffering.
Psylocke, Quill, Spike and Multiple Man are all associated with some branch of the X-Men franchise in the comics, but in X-Men: The Last Stand, they all appear as members of Magneto's Brotherhood of Mutants.
Henri Ducard (Liam Neeson) proves himself a ruthless villain in Batman Begins. In the comics, he's not really much more than a cynical French detective (whereas the movie leaves his nationality ambiguous). While the comic book Ducard is certainly an unsavory figure (in addition to being a Misanthrope Supreme, he's a sociopath who has no problem with shooting enemies In the Back), he's far from being a supervillain and will even help Batman and Robin if he believes it is in his interest to do so. Batman Begins turns this character into a genocidal lunatic...although the plot eventually renders this forgivable by revealing that "Henri Ducard" is nothing more than an alias for Ra's al Ghul, another comic book character who is portrayed more or less accurately, and possibly with more sanity than he deserves, since the relatively-realistic setting cuts out Lazarus Pits.
Comics Ducard is a killer, and was a really, really bad father—something that has returned in the New52, with a villain called Nobody who turned out to be the son Ducard disowned all those years ago for losing to the young Bruce. Bruce's son kills him.
In the comics, Ra's al-Ghul's daughter Talia is a gray-shaded character constantly going between Anti-Hero and Anti-Villain, and has sincere feelings for Batman. In The Dark Knight Rises, Talia is a flat-out villain with none of the moral conflicts she has in the comics, instead being just as much of a Knight Templar as her father. And her feelings for Batman are revealed to have been all an act: she never loved him, she loved Bane, the supposed Big Bad of the movie, who is actually her Dragon.
Bane himself, possibly, depending on whether you think the version that occasionally verges on Noble Demon but doesn't care about anyone but himself is more or less evil than the nihilist with the bomb who does everything for Talia.
While Velma Von Tussle is the villain in all versions of Hairspray, she is portrayed as a considerably darker character in the film, which shows her rigging the Miss Hairspray pageant, attempting to seduce Wilbur, and even implying she may have murdered her husband for startup money ("He... accidentally suffocated himself"), none of which she did in the original stage musical. This is also apparent in her ultimate fate in each version: in the film, she is taken down by Wilbur and Edna in an Engineered Public Confession, while is the show she does a last-minute Heel-Face Turn due to The Power of Rock.
Two American film versions of Les Misérables came out in periods of major hysteria about Communism, one in 1935 during the First Red Scare and the other in 1954 during the Cold War, and both of them portray Enjolras in an incredibly negative light, as a dangerous fanatic who co-opts Marius's nonviolent protest movement and turns it into a bloody rebellion. The '34 version even cast John Carradine, better known for numerous turns as Dracula, in the role. In the original novel and more accurate adaptations like the stage musical, he is of course the leader from the beginning and a borderline Messiah, and what's more, Marius isn't even all that die-hard of a follower. This change was quite obviously made because nobody would have accepted a violent revolutionary as a hero at the time.
Inspector Javert, while not that nice to begin with, is much more cruel in quite a few adaptations (such as the 34, 35, 52 and 98 versions).
In Warren Ellis' Extremis storyline, Aldrich Killian is a normal civilian scientist who becomes wracked with guilt and eventually commits suicide after selling the Extremis formula to some domestic terrorists. In Iron Man 3, he's a Smug Snake and one of the major villains, and is also the founder of AIM, as well as the true Big Bad of the movie, Word of God and Killian's own boasts stating he's the real Mandarin..
His right-hand man Eric Savin was never outright villainous in the comics as he is in the film. In the comics, he's the cyborg anti-hero Coldblood.
The Mandarin , or rather Trevor Slattery, is an inversion as he's nothing but a fraud. However, according to Word of God, Killian, not Slattery, is the real MCU version to the Mandarin (as well as the Scientist Supreme of AIM). Killian in the comics is just the co-creator of Extremis, commits suicide early on, and isn't villainous at all.
As of the Marvel one-shot All Hail The King, neither Trevor nor Killian are the real Mandarin. The real Mandarin is a mysterious and legendary Asian villain from whom they both just borrowed the name. He may or may not show up in future stories.
There are a lot of film adaptations of Frankenstein in which the monster is portrayed as, well... a monster. In the original book, Frankenstein's "monster" is actually a tragic, erudite victim of circumstance. Frankenstein himself is also a complex character with plenty of sympathetic moments, but many films portray him as a two-dimensional cackling Mad Scientist.
Bishop Manuel Aringarosa, the head of Opus Dei in The Da Vinci Code, was originally just an unusually conservative clergyman who got roped into helping The Teacher out of desperation, since the Catholic Church was planning to disown Opus Dei and he needed help to keep it afloat. The film version makes him a member of a splinter cell within the Church that actively wants to find and destroy Mary Magdalene's remains to hide the truth about Jesus' descendants, and it has him manipulating Fache (an Opus Dei member in the movie) into hunting down Langdon despite his innocence. Notably, the book gives him a happy ending, where Fache realizes that The Teacher manipulated him and ensures that he goes free. In the movie, he's last seen being arrested by an angry Fache and hauled off by the police.
In The Beast from 20,000 Fathoms, the title dinosaur rampages in New York, destroys Coney Island, and kills many people in the process. In the short story that the movie is inspired by, "The Fog Horn" by Ray Bradbury, the creature is a much more sympathetic and tragic figure, coming to a lighthouse because it mistakes the horn for the cry of a member of its own species. Although it destroys the lighthouse in a rage when the horn is turned off, no one is killed, and it returns to the ocean in peace. The human characters even remark that this turn of events is for the best, as it spares the dinosaur from wasting its feelings away on something that can't return them.
Alistair MacLean's novel The Satan Bug has a climax taking place aboard a helicopter. In the book, the pilot is an innocent bystander forced by the villain to fly the copter for him, and he and the hero cooperate to defeat the villain. In the movie, however, the pilot has become a henchman of the villain and even tries to kill the hero.
Sab Than from John Carter. In the book, he gets very little characterization but comes off as something of a Worthy Opponent, while the movie version is a straight-up villain. This is due in part to his being a Composite Character of book!Sab Than and his father, Evil Overlord Than Kosis, as well as the emphasis on the Helium vs. Zodanga conflict (Sab being the leader of the latter).
Star Trek: Into Darkness gives a darker view on Khan's origins. In the original series, Khan's origins depicted him as a "benevolent tyrant" who was repressive but not wholly murderous (though he may have just been a Villain with Good Publicity; its rather odd, but nobody in Starfleet had even heard of the guy, even though he was supposedly a prominent warlord). Into Darkness has Spock state that history indicates that Khan and his followers were planning to destroy those deemed inferior. Khan doesn't confirm it but doesn't deny it either.
While we never knew what Admiral Marcus's intentions were in the original series, it would be safe to assume he wasn't a Manipulative Bastard who wanted to start a war with the Klingons.
In most film adaptations of The Three Musketeers, Rochefort is turned into The Dragon and is usually killed in a climactic fight with d'Artagnan. In the novel, he insults d'Artagnan and steals his letter of recommendation in the beginning. He barely appears in the rest of the story. Occasionally d'Artagnan spots him and tries to chase him down to have a duel, but never catches him. At the end, Richelieu orders them to become friends, which they eventually do after several non-lethal duels. The Musketeer even elevates him to Dragon-in-Chief and makes him the killer of D'artangans' father (well, the character is named Febre and Rochefort is actually in the film as well seperately, but Febre is clearly based on Rochefort, so this is just a case of Decomposite Character).
For that matter, Richelieu himself is probably one of the biggest examples in all of fiction. Several adaptations make him out to be the Big Bad with diabolical intentions when in fact the original novel portrayed him as an Anti-Villain at worst. He's not exactly a good guy and he is a devious schemer, but he's more interested in making sure that he has more influence over the King than the Queen or anyone else does, and...that's about it. He's willing to commit some small crimes and immoral actions to get that far, but he isn't trying to have the King or Queen murdered or attempting to take over the country. Doubles with Historical Villain Upgrade as well, since the novel version is much closer to the Richelieu of real life. The actual villain of the original story ends up being M'lady de Winter, Richelieu's actualdragon who he eventually decides is a dangerous liability because she's a dangerously homicidal Manipulative Bitch.
The book version of The Shining makes Jack more sympathetic than in the movie and he ultimately redeems himself and doesn't kill anyone in the book. It was this factor that launched criticism from its creator, Stephen King.
The 2005 film adaptation of The War of the Worlds presents Harlan Ogilvy as a violent madman. In the book, Ogilvy is an astronomer who, far from being violent, was the narrator's friend who was killed by the Martians early on during an attempt at communication. The character's more antagonistic and unhinged personality comes from the deranged curate that the narrator meets in a cellar, not Ogilvy himself.
The 2005 TV movie version of Hercules made the artistic decision to not ever show the Gods and keep their actual existence ambiguous, since Hera was the cause of most of Hercules problems in the myths they had to work around this by making other characters in Hercules life antagonize him as worshippers of Hera. This included his mother Alcemene, his first wife Megara, and his half-brother Iphicles, none of which antagonized Hercules in the original myths.
In The Wonderful Wizard of Oz the Flying Monkeys were neutral and were bound by an enchantment to serve the Wicked Witch of the Westnote She owned the Golden Cap, which meant that she could command them three times - they even serve Dorothy once the Witch is destroyed. In the film they are the willing servants of the Witch.
The Witch herself counts too, sort of. In the book, she does not appear until near the end where Dorothy and the others are told to retrieve her broomstick. The film expands her role to make her the lead villain, wanting revenge on Dorothy for the death of her sister the Witch of the East.
In the Superman comics and Superman II, General Zod is a charismatic military leader that only fought when he saw fit, and tended to use his powers for spectacle. In Man of Steel, Zod is a remorseless mass murderer that is willing to commit genocide and destroy everything in his path to accomplish his goals. He even manages to kill Jor-El before his imprisonment. In most previous adaptations, Zod is stripped of his powers or otherwise incapicated, but in Man of Steel, Superman is forced to kill Zod when he tries to use his powers against defenseless bystanders.
In the Thor comics, Algrim/Kurse does work for Malekith for a time, but Malekith betrays him and Algrim—a noble soul—swears loyalty to Thor and Asgard, in fact being the one to kill Malekith himself. In Thor: The Dark World, Malekith does sacrifice his own people but doesn't betray Algrim personally. Algrim has Undying Loyalty towards his master and becomes Kurse as a result. The sons of Odin ultimately have to kill him to curb his brutal assault.
The film adaptation of Beowulf portrayed Beowulf as being seduced by Grendel's mother, lying about it, and having the dragon with her. Also, King Hrothgar is Grendel's father, something he wasn't in the original poem.
Film and TV adaptations of the Iliad, AKA: The Trojan War, tend to play up the villainy of the Greeks while portraying the Trojans in a more sympathetic light - despite the fact that it was their younger prince, Paris, stealing Helen, wife of the Greek warrior king Menelaus, that started it. The 2004 film adaptation, Troy, in particular went to great lengths to portray both Menelaus and his older brother, the supreme king of Greece, Agamemnon, as the bad guys, Agamemnon in particular comes off as a shallow, superficial, one note mustache twirling bad guy. Now in the original poem Agamemnon's not exactly a nice man to begin with, but in the 2004 film he's practically a Nazi.
In the original film, Gort the robot was an enforcer of peace, generally not attacking until Klaatu was threatened. In the remake, GORT, who is actually a Swarm Of Alien Locusts designed to only attack people and things made by people, is the aliens' method of destroying the human race.
Cirque Du Soleil Worlds Away: The creatures that emerge from the sand to spook and separate Mia from the KA good guys here are comic relief in the original show.