Beatrice has turned into this, starting out as the Card-Carrying Villain of the series, gloating over new ways to sadistically kill Battler's family and screw with his head before gradually losing her dignity and becoming one of the biggest Woobies in the series apart from Natsuhi. For starters, at the end of Ep 4, she is impaled with several blue wedges but cannot die because Lambdadelta has shackled her to the game for all eternity. As a result, in the beginning of Ep 5, she becomes an empty shell who can't do anything by herself — she can't eat or speak, hell, she can't even lift up a cup of tea. And to make matters worse, when Battler tries to come up with an explanation to the mysteries that denies the involvement of magic, she suffers. Bernkastel, being the charming person that she is, makes a point of saying so. And to top it all off, after having her former title stripped, she is sentenced to a rather horrible death by Lambdadelta and Bernkastel, and tries to go down laughing but ends up sounding like a human denying agony (which, sadly enough, she is), and even when Battler steps in to save her, he loses, and she begs him to not leave her alive. And who could forget her touching death scene? And then, in Ep 6, after being revived with no memories of her former self or her game with Battler, she gets treated like dirt by Battler all because she doesn't act like the Beatrice he knew. It's all you can do to not want to give her a hug. Not to mention, she was actually helping Battler all along, and just wanted him to figure out the mystery and remember his promise to her. Episode 7 puts all of the above in the perspective and only ups her Woobie-ness aspect Up to Eleven.
Rosa Ushiromiya. It's pretty hard to deny just how screwed up her life is, and, at least as far as we know at this point, how relatively little of it is her fault. Of course, it doesn't change the fact that she treats her daughter, Maria, miserably.
Eva Ushiromiya. She treats Natsuhi, her long-suffering sister-in-law, and Shannon, the object of her son's affections, like crap...and then we get flashbacked to her youth and find out that she pretty much got the exact same treatment from Kinzo, right down to the "borrowed womb" speech she gave to Natsuhi. She's one of the few siblings who is Happily Married and adores her son, but in half of the murders, she loses one or both of them and utterly snaps. In the Bad Future of 1998, not only is she suspected of murdering her family (being the sole survivor of Rokkenjima), but Bernkastel manipulates her relationship with Ange; Eva treats Ange like crap to hide the truth about her parents, and dies with Ange thinking that she's a selfish psychopath. Not to mention that she has a power-hungry Literal Split Personality who loves to make her suffer. Eva's life SUCKS. Perfectly illustrated here.
A good portion of the characters in Umineko qualify as this actually, as most are abused and broken down by life while still remaining in some way awful. Lambda, Erika, Rosa, Natsuhi, Eva, Krauss, and especially Beatrice /Yasu/Shannon are perhaps the best examples.
Although it's often overlooked due to inherent awesomeness, Archer in Fate/stay night is quite woobilicious and also quite the asshole. Before switching back to the good guys, his rather brutal nature is quite apparent. Even apart from any violence, his attitude and speech are also quite a bit darker and more straightforward than any of his allies. Much of this is quite Harsher in Hindsight, considering both his backstory and just who, exactly, he is.
Yet another 07th Expansion example, proving that Ryukishi 07 is fond of this trope: From Ookami Kakushi, we get Sakaki. While he may hold a horribly racist attitude towards the Kamibito, abandons Hiroshi or outright kills him in one end when he refuses to go along with his plans, and starts a town war to massacre the Kamibito in the story’s true end, he has also been put through his share of tragedy: He lost his fiancée to the old laws of the town, found her mutilated corpse, and has spent the past four years feeling as though he has no real reason to be alive other than for the sake of living. The only thing that gives his life any purpose at all, according to him, is the thought of avenging his fiancee’s murder. His arc, in particular, is a master with this trope, showing him at both his most despicable and most sympathetic.
Franziska von Karma. Despite her rash demeanour in court, you've got to wonder what it was like to be raised by Manfred von Karma.
Miles Edgeworth in the first iteration qualifies as well, with the death of his father (which he, due to the circumstances, blamed himself for) and being raised by Manfred von Karma.
Godot/Diego Armando is one. Yes, he is quite a jerk to Phoenix and his plan of dealing with Morgan's plan to kill Maya was self-centered but he has poisoned by Dahlia, had his lover be killed while he was in a coma, and going through medical treatments just to say alive. He's pretty much a huge Stepford Smiler who hides much despair and guilt in which it was a surprise that he can show up to court.
Even Dahlia Hawthorne can be seen as one, and is by her sister Iris. The sisters were separated from their mother and raised by their father, who showed no love for them and sent Iris off to Hazakura Temple merely so that the inheritance would not have to be divided. Iris points out that the reason she didn't become like Dahlia is because Sister Bikini was her Parental Substitute, while Dahlia had no one of the sort.
Phoenix Wright: Ace Attorney – Dual Destinies gives us Simon Blackquill, who spends much of the game as a standard asshole prosecutor, who also happens to be in jail for murder. Then, it's revealed that seven years ago, his mentor was killed and he walked in to apparently find out that her daughter (who he was said to get along with very well) did it. In order to protect said daughter, he framed himself for his mentor's murder, putting himself on death row in the process and turning cold, cruel, and sarcastic during his incarceration.
There's also Simon's sister Aura. She not only has to watch as her brother ends up on death row for a murder he didn't commit, but the victim in that case was her esteemed colleague, (whom she strongly implies that she was in love with). On the jerkass side, she's ill-tempered and confrontational, beats up the robots she and her colleague made, and holds several people, including the main character's daughter, hostage in order to try to get her brother's conviction overturned (the day before he is to be executed), although she releases the hostages and turns herself in, once he gets off.
Hatoful Boyfriend's Sakuya Le Bel Shirogane. A racist, ableist Upper-Class Twit and royal snob of the highest order... who's troubled by loneliness, having been taught to push away anybody "lesser" than himself, and wants more than anything to pursue a career by his own abilities, rather than abide by and perpetuate his family's tradition of nepotism and bigotry. The woobie side shows most in his route and in the nonromantic "Bad Boys Love" route, where he learns that his birthright is a lie and then watches his brother Yuuya die of poisoned wounds sustained defending Sakuya himself, despite the bad blood between them due to Yuuya being born of their mother's (mixed) first marriage.
Brin, the Duchess of Hellas, is very manipulative, arrogant and trying to start a war purely for her own gain. She was also dumped by no less than THREE lovers. The last one, who she thought would always be with her, dropped her for being "too challenging" and then ran off with a priestess.
Kevan, the temperamental Earl of Io, seems to be fueled only by rage and turns into a Leeroy Jenkins whenever his family seems to be even remotely threatened. He kills people without having proof of their guilt and honestly doesn't seem to care much about their innocence. Turns out that the reason for his behaviour is that he was sexually abused by his stepfather from his early teens (possibly preteens) until the day his younger half-brother Thaddeus walked in on them, traumatising the poor kid and driving a serious wedge between the family. His mother eventually had the stepfather killed, but Kevan, suffering from Stockholm Syndrome, became estranged from her and moved in with his older sister. The two then proceeded to develope a very unhealthy incestuous affair. Elodie can interfere and possibly redirect his fanatical loyalties from his family to herself, but all she really succeeds in is becoming his Living Emotional Crutch and it is strongly suggested that he would kill himself should anything happen to her..
Elodie herself can become this depending on how you play. She can perform the most cruel acts; ordering numerous executions, abusing servants and burning people alive. But sometimes you can't help but wonder if she simply cracked under all the pressure of being a 14-year-old-almost-Queen with a target painted on her back. On the other hand, she can also go completely beyond the pale by either killing her father to become the Big Bad's minion, or sacrificing her adorable cousin to a kraken in order to save her own ass.
Absolute Despair Girls has the Warriors of Hope. They're a group of 5 children that indiscriminately murder defenseless adults and teenagers as a game. Each one has also suffered prolonged, harsh parental abuse and/or neglect to the point where they had to be saved from attempting mutual suicide.
While Toko is antagonistic towards people and assumes the worst out of people, she was constantly bullied back at her old school causing her to have low self-esteem. Not to mention the fact that she has a Serial KillerSplit Personality making it seem that she pushes people away from her just to keep them safe.
After the second chapter of the second game, Fuyuhiko becomes this after he found out that his sister was dead and Peko got executed for committing a murder that she thought was her just following Fuyuhiko's orders to kill the accomplice for his sister's killer
Ittosai, Yo-Jin-Bo's resident Psycho for Hire who spends most of his time insulting the rest of the cast. If you follow his path through the game, you eventually learn that his father was the one who messed him up terribly as a little kid in order to turn him into a bloodthirsty killing machine, even though he hated it. By the time he becomes The Atoner, you're glad that Sayori is there to give him lots of hugs.