Yamato Tachibana from Inyouchuu is the main page's image. He's a Half-Human Hybrid who spent much of his life as an outcast, traveling around Japan with Yayoi in order to find a cure for his demonic tendencies. The Shiratori twins, Mikoto and Takeru, were some of the few people to actually treat him decently (Belligerent Sexual Tension with Mikoto notwithstanding). In the third game, both girls allow themselves to be impregnated by demons in a last ditch attempt to keep Yamato's demon side from going out of control, and in a bad ending are raped and murdered by the untrusting villagers who want to kill him. Needless to say, Yamato loses it - it doesn't end well for the villagers.
The secret character from Nameless has been trapped in a closet for countless years, and the most important person in his life doesn't even remember him. This doesn't stop him from straying into several shades of Yandere on his quest to recover some of his life, however. He does grow to regret his actions near the end, however.
Sakura eventually decides (with the help of the devil that is possessing her) that since her life sucks so much, she's just going to kill everyone she doesn't like, and then give birth to the devil. Well, the last part probably wasn't too high on the agenda but she didn't really care if it happened or not.
Surprisingly enough, Angra Mainyu, aka Avenger, also qualifies. He was originally just a man who was tortured to death by the people of his village to serve as a scapegoat for human evil, which technically fulfilled the requirements to become a Heroic Spirit. This means that even after dying he can never be reincarnated and must bear the memories of his life for the rest of human existence. He justifiably hates humanity as a consequence.
Rider/Medusa also counts, throughout the whole series. Her past involves getting bullied by sisters as well as humans, being cursed by the gods, and turning into a monster. Her resolve in joining the war is simply to protect Sakura simply because they're kindred spirits. Too bad that Sakura handed down the Master status to Shinji and Rider also suffered his abuses, but since it's what Sakura wanted and all to protect her, Rider had to embrace her status as a 'villain'.
Kohaku of Tsukihime has become so emotionally broken that she thinks of herself as a doll and has no idea how she really feels about anything. Oh, and she's plotting the deaths of Akiha and SHIKI, is implied or perhaps stated to be involved in Makihasa's death, and may view Shiki as a target as well, though she doesn't succeed there in any path. It's okay if everyone dies except Hisui. Oh, and she's indirectly behind all the serial killing going on in the Far Side routes.
In Analogue: A Hate Story we discover that *Hyun-ae, known as the Pale Bride when she was alive was this. She was a modern Ill Girl who, after being awaken from cryogenization discovers herself in a world where they got backwards to a sexist, misogynistic civilization. She then was so abused, physically and mentally (including having her tongue cut so she couldn't backtalk any men never again), that you couldn't feel surprised when after an ill worded advice too many she finally snaps and decides to upload her consciousness to an AI and override the system to turn off the life support, killing everyone on board including herself.
Nine Hours, Nine Persons, Nine Doors has Akane who, as a child, was kidnapped, forced to play the Nonary Game, and ended up burning to death in the incinerator. Through use of telepathy and time travel, some version of her manages to survive to present days, where she and her brother abduct seven other people involved in the last game and submit them to psychological torment (they lead them to believe they had bombs implanted in them, and that they'll all be drowned within a time limit). She also uses the game as an excuse to murder the four men responsible for her death.