In Disney's Treasure Planet, John Silver is supposed to be the bad guy; and he does it pretty well, most of the time. But he also turns out to be a great father figure to Jim Hawkins. Although he did intend to find the treasure, it was hinted that he didn't want any innocents killed because of his attempt, which resulted in him telling off Scroop when he murdered Arrow while making it seem as though Jim Hawkins caused his death due to negligence on his part.
M starred Peter Lorre in the role of Hans Beckert, the first Serial Killer in all of film and an implied pedophile, and one of the most pitiable villains ever portrayed.
For that matter, the fraternity of criminals who take it on themselves to track him down is, at some points, almost indistinguishable from the actual police. Even to the point of throwing him a "trial", which they somewhat bleakly joke is legitimate because they're all legal experts, what with so much experience with the judicial system. Then they almost tear him apart...
Which leads to an epic Reason You Suck Speech by Beckert himself, who asks the fraternity what right they, "lazy bastards" who commit crimes for things they could have avoided if they learned a decent trade, have passing judgment on someone who is compelled by powerful impulses to do the things he does "against his will". He seems to genuinely hate himself for what he does as much as anyone else.
In Spider-Man 3, the Sandman is a very sympathetic villain - he's not too smart, and he's made some bad decisions in his life - but ultimately for good reasons; namely, getting enough money to treat his daughter's illness. In the end, he and Spider Man part ways, agreeing that their mutual animosity is doing nothing but making them both unhappy.
Doc Ock in 2. Altruistic guy, working for "the good of mankind", accidentally kills his wife and turns himself into a monster with no inhibitions, and fixates on his dream, still believing that he is trying to help humanity, when he is actually constructing the means to destroy half of New York City. Sure, when he's evil, he is VERY evil (threatening to kill old ladies and a train full of people for example), but in the end, it's shown that he's still a good guy deep down. "I will not die a monster."
Most of the evil stuff the guy does is a result of the intelligent AI he designed into the claws affecting his brain. It was designed with the sole purpose of creating the cold fusion device, and a point is made to say that when the chip at the base of his spine is destroyed (which it was) it would be capable of controlling him.
Prince Nuada in Hellboy II: The Golden Army. Nuada is striking back at humanity because it is destroying his world. Nuada insists, and the film supports, that the world will be a worse place without his kind. Director Guillermo del Toro notes that Nuada has more morals than most of the heroes, notably Abe and Liz, who both place their own love before the fate of the world. Although Nuada is also a hypocrite and somewhat Ax Crazy.
Fredrick Zoller seems like the most conventionally heroic character in Inglourious Basterds until his very last lines. He's brave, humble, seems like a Dogged Nice GuyRomantic Comedy protagonist while courting Shoshanna, and is repulsed by the sight of himself killing man after man in Goebbel's propaganda movie about him. Too bad those last lines carry a strong implication that he was about to force himself on Shoshanna before she shot him.
Perhaps a stretch, but Vaako, the Noble Demon from The Chronicles of Riddick, comes off this way at times. He's surprisingly competent, genuinely believes in the Religion of Evil, shows signs of Honor Before Reason, and, to the surprise of everyone, doesn't attempt a Klingon Promotion on the Lord Marshall (well, not until his wife convinces him that the Lord Marshall has violated the Religion of Evil). And when Riddick defeats the Lord Marshall, rather than attempting a Klingon Promotion by killing a distracted Riddick on the spot, Vaako is the first to bow to Riddick and proclaim him the new Lord Marshall, since Vaako has no justification to attempt to wrest the throne away from Riddick.
In The Rock, Ed Harris' character is an American hero who is motivated to get the government to acknowledge the sacrifices of soldiers who died during black ops. Ultimately, he reveals that his whole terrorist scheme is a bluff, but his mercenary colleagues are not as noble.
The bank robbers in Inside Man are doing it to get even with a former Nazi Collaborator. They have scruples that involve not hurting or killing anyone, and not stealing cash from the bank but only some diamonds from a man guilty of war crimes. They freely admit they are no martyrs but don't fit under the label of plain old villains either.
Roy Batty was nothing if not this trope; all he wanted was a way for himself and his fellow Replicants to live longer than the four years allowed to them.
Believe it or not, Hitler in Downfall, though his actions were not exactly noble, per se. He's portrayed as a broken man. Many were offended that Hitler could ever be portrayed sympathetically, but the directors defended it by saying that they were portraying him as a three-dimensional person and not just doing it For the Evulz.
Between his paranoia, uncontrolled sobbing, and screaming that the German people all deserve to die for failing him, the directors were really trying to reveal him to be a pitiful, mentally ill waste of life, rather than a diabolical supergenius warlord which the mainstream media likes to portray him as.
The original Scarface, the one from 1932, has an Anti-Villain as its titular character, who literally pets the dog at multiple points in the film. It was very controversial at the time because of this.
Sybok from Star Trek V: The Final Frontier uses his powerful telepathic abilities to cure people of their deepest emotional pain in order to win them over to his side and help him achieve his goals. However, he truly believes he is using his therapeutic powers out of kindness and a sincere desire to help, and denies that it is a means of controlling his victims' minds.
The villains of The Adjustment Bureau aren't really very evil. They explicitly state that, if they succeed, one protagonist will be world-famous and the other will be President. They are genuinely interested in helping and their version of the world really is better for all involved. The most villainous thing they do is make threats and cause a minor injury.
Lestat in Interview with the Vampire. He's controlling, egotistic, selfish, and proud; he also proves to be Claudia's main obstacle to freedom and Louis goes between tolerating him and flat-out hating him. But at the same time, he's easily the most fascinating character in the story and his attitude sets him apart from other actual antagonists encountered later.
Chip Douglas from The Cable Guy. His creepy and obsessive stalking of the main character is driven by the fact that he's been socially isolated for his entire life and is desperate for somebody to be his friend.
Robert from Mystery Team. He didn't want Brianna's parents to be killed, and took her and her sister in. He didn't even interfere with the Mystery Team. That said, his motives are rather sinister, risking the lives of thousands of employees and customers to save money.
The Operative from Serenity is a man willing to do whatever it takes to get the job done, and is perfectly willing to even kill children if it serves his purpose. However, he readily admits that his actions are monstrous and that he's working towards a better world that he has no place in. He's just doing what he feels needs to be done, to create the utopia and world without sin that the Alliance is building. When he sees exactly what the Alliance has been building, he abandons them completely.
Loki, the villain from Thor, is continuously doing the wrong things for the right reasons. He sneaks the Frost Giants into Asgard to show his father that Thor is not ready for the throne, brings the Frost Giants back to Asgard in order to kill their king, Laufey, and tries to destroy Jotunheim because he believes that if he destroys Asgard's enemy, his father will finally be proud of him.
John Hammond in the movie version of Jurassic Park. In the book, he's a regular villain for in it for the money.
