Dragon Bones has Garranon, whose motivations are noble (he wants to protect his brother), but who is ready to do everything for that goal - he openly admits that he would torture puppies to ensure the safety of his brother.
Cujo isn't really a villain in the popular sense of the word, but he's just as much a victim as anyone else is, and if the Cambers had taken the possibility of their dog catching rabies seriously, the disaster could have been avoided. Parts of the books are told from his perspective; there it's shown that he suffers horribly from rabies, and only attacks people because he believes that they are responsible for his pain.
Claude Frollo from Victor Hugo's The Hunchback of Notre Dame suffers from his obsessive love for Esmeralda, which causes him to go tragically insane. What makes his suffering sympathetic is the fact that he was a deeply compassionate and caring man before he laid eyes on the gypsy.
Mordred in some King Arthur interpretations, especially where (as some legends have it) Arthur tries to have him killed at birth as a threat, he's raised to hate Arthur by his mother, and hated in turn by Arthur's supporters simply because he exists, leading to the inevitable clash. It's hard not to sympathize with him in many cases given that.
Murtagh. During Eldest, he is enslaved by King Galbatorix and forced to fight on his side. Brisingr makes it appear that he's gone completely evil at first, but Eragon speculates that he's getting back at the world for giving him a crappy life. Near the end of the book, he's fighting the Dragon Rider Oromis and he desperately screams at him "YOU COULD HAVE HELPED US!".
His dragon, Thorn, counts as well, as he wonders why he was brought into the world just so he could be tortured and destroy things.
Galbatorix's dragon, Shruikan, is one of these as well. While Galbatorix remains a villain, several characters point out that Shruikan never chose to serve him; his real rider was killed when he was a hatchling and he was forced to bond with Galbatorix, driving him insane. When he finally appears in Inheritance, he is a nightmarishly huge and powerful dragon that appears to be an Omnicidal Maniac; Elva tells Eragon that nothing is left of him but pain and hate, and the best they can do is end his suffering.
The entire town of Dark Falls in the first book. They were all once a normal, thriving community, but an accident at the nearby chemical factory caused gallons of toxic gas to engulf the citizens, transforming them into vampiric mutants. Now, they have to feed on new visitors every year to survive. At the end, after the protagonists have destroyed most of the residents, the real estate agent responsible for ensuring new victims is the only survivor. The ending implies he'll continue his gruesome business, all alone.
The creature from Frankenstein is driven to evil when everyone (including his eponymous creator) rejects him because of his monstrous appearance. In the end he tries to take his revenge on humanity before committing suicide.
(Only in the book; the movie adaptation replaced all this with "Science Is Bad".)
The Hunger Games: Just about any of the other career tributes. Yes, they are all ruthless and one even taunts Katniss about Rue's death but they are all teenagers being forced to fight to death in a Crapsack World.
The ruthless Tywin Lannister of is the most feared lord in Westeros. He is this because his father's weakness almost caused the fall of their family. The death of his wife (who was the velvet glove to his iron fist) also made it hard for him to raise his children with love and compassion, and led to his hatred of the child of this birth, Tyrion Lannister. Unfortunately, he has gone to another extreme, which made his children very screwed-up, and ended in his death.
Prince Viserys of House Targaryen lost almost his whole family in a rebellion that toppled their dynasty and had to sell whats left of their riches so he and his sister Daenerys can survive. Drink and years of being treated as a joke caused him to threaten Dany in front of her husband Khal Drogo who then killed him.
Theon Greyjoy was taken hostage as a child by Ned Stark after his father's failed rebellion. He betrays the Starks to earn his father's respect but can't because the man sees him as a "greenlander". With no one to back him up, Theon is captured, tortured and flayed and becomes "Reek".
Gollum of The Lord of the Rings was a good person before being corrupted by the One Ring. After Gollum's death, Frodo still feels sympathy for him even though he betrayed him and Samwise.
Alistair Mechanus of Heart of Steel is undeniably a villain, what with the plans for world conquest and everything, but he only suffered a psychotic break when he discovered that the parents of his comatose girlfriend—whom he'd loved more than life itself—was forced to take her off life support because they could no longer afford to keep her alive. He'd missed saying goodbye by about a week, after spending five years rebuilding himself after the car accident they'd both been involved in.
Carrie has a horrible abusive mother and is bullied at school by the cruel Chris Hargensen. At prom, Chris dumps pig blood on her, and the jerkass people at the prom laugh at her. Driven over the edge by her torment, Carrie goes on a rampage tthrouhout the town, killing hundreds of people.
Tales of Dunk and Egg has Daemon Blackfyre II who tries to start a rebellion but he is just a pawn by other nobles and his support evaporates when he loses a jousting match. He possibly spent the rest of his life as a prisoner in the Red Keep.
Ephemeral Prince expands on the backstory of the antagonists of the prequel game and reveals they were victims of the novel's antagonists, the lords.
Lina was locked in a tower for most of her youth because of a prophecy that her child will destroy the world. She experiences a Hope Spot when Edgar rescues her and the two become the rulers of the prosperous kingdom of Sabine. Unfortunately, the lords didn't approve of the prophecy or their marriage, so they destroyed the kingdom as Disproportionate Retribution. This causes the couple to become cynical and paranoid to the point where they abandoned their responsibilities as rulers and parents to gain power for themselves, ironically setting up the circumstances necessary for the prophecy to come true. They go on to become the secondary antagonists of the prequel game. Of the two, Lina is more tragic due to having some regrets about what they did to their son, Snowe.
Soan (the Original King) and Xiri (the demon inside Snowe), the Big-Bad Ensemble of the prequel game, ended up in their situation because the former was tricked by a lord into eating the latter alive. As a result, Xiri goes insane and convinces Soan that the only way to make his kingdom immortal is to kill his citizens and take their souls. This fails to make any headway into Soan's research into immortality and he clearly regrets what he did to his people, but he stays in denial that his plans are beyond salvageable. Unfortunately, both of them end up in worse situations when Edgar and Lina separate them and haphazardly seal Xiri into Snowe, causing Soan's citizens to die and causing Xiri to further lose his sanity. Soan himself eventually recovers from their attack and snaps from losing his only hope of reviving his people, though losing to the main characters causes him to calm down and realize his folly.