Gunther Hermann in Deus Ex. While, like his partner Anna, he is a killing machine, it would appear that he has been handed the short stick in life, and he apparently had feelings for Anna, as he relentlessly hunts down JC after he kills her. A diary entry in the cathedral level mentions that the author heard him crying once.
A Renegade Shepard can be this. S/he's an asshole, but s/he also has been dead for 2 years, and if you picked Ash or Kaiden, s/he also gets dumped. Poor Shepard. Oh, and Liara has...changed, which also has the ability to make him/her a Woobie.
Jack! Nothing in that woman's life has gone right, leading to us nearly forgetting that it's turned her into a Sociopathic Hero with a persecution complex. It's also worth mentioning that the player can effectively turn her into even more of a woobie. She has been used and abused all her life and believes that everyone in the galaxy is only interested in themselves and what they can get out of other people. If Shepard chooses the Renegade sex option when she confronts him, that just confirms her belief, meaning she will continue to forever circle the drain of self destruction, making the realization that you could have been her first true friend and yet refused so much worse.
Miranda is rude, harsh and cruel, especially towards the aforementioned Jack and is also a member of a racist terrorist organisation... She was also raised by an abusive father who would have killed her if she wasn't perfect and also made it so she couldn't have babies, which was what she most wanted.
Kain of Legacy of Kain could be the poster boy for Villain Protagonist, being the main protagonist of the series and a cold, bloodthirsty, manipulating, selfish schemer. However, he's only this way because he's learned that everyone in the world, stretching back and forwards through time, wants him dead. Why? Mostly because it it's Kain's destiny to save the world by conquering it (long story), and a lot of people are trying to take over Nosgoth too. This leads to him staking the existence of the space-time continuum to reclaim his proper destiny that others have robbed him of. His incredibly selfish and jaded outlook is spawned partially by all this, and partially by the fact that he was corrupted with the insanity of Nuprator just seconds out of the womb and so was pretty much ascertained from birth to grow up to be a bastard.
Silent Hill 4: Walter. As mentioned on the Anti-Villain page, it's hard to decide whether or not you want to kill him because of what he did or because he needs to be put out of his misery.
Also, Cynthia. Yes, she might have been a bit of a bitch, but did she really deserve that?
Jamie Washington from Splinter Cell: Double Agent. He has no real redeeming qualities, but he's just so trusting and devoted to Sam that it makes you feel bad for him knowing you'll, as a double agent, eventually kill him. Even his Last Words before being killed by Sam are to claim he knew Sam wasn't a traitor.
Yosuke of Persona 4. A lonely teenager who is also the game's resident Butt Monkey. The girl he loved is murdered (possibly raped beforehand) and he finds out that she hated his guts when he goes to investigate. Most of the town hates him because his parents managed the new large chain store, driving out the local businesses. On the other hand, his social skills are nearly non-existent; his foot is pretty much permanently lodged into his mouth and he can never seem to tell when his comments or jokes cross into insensitivity territory.
Yukari from Persona 3. She's a Tsundere, she's normally nice, but can be very snarky on a bad day and, as seen in The Answer she is quite capable of stubornly making choices that would doom the world. However, her father died trying to prevent The Fall. The video containing his last words and instructions on what to do to prevent The Fall was doctored by Ikutski and used to make him take the fall for the Dark Hour, and to trick SEES into helping bring about the very thing he tried to prevent. Her mother began throwing herself at other men in order to fill the void. And the boy she fell in love with, the main character, died in Aigis's arms before she could be there for his last moments.
Morrigan of Dragon Age: Origins has had no human contact except for her uncaring and sometimes cruel mother for her entire life and has spent a lot more time as an animal than as a human. Her trust issues and pragmatism-at-the-expense-of-compassion attitude follow naturally.
Fenris from Dragon Age II won't pass up an opportunity to remind everyone how horrible and dangerous mages are and how magic spoils everything it touches. He happens to be an escaped slave from a country run by power-hungry mages and lost his memory of everything that happened before the ritual that gave him his lyrium markings (which amplify his fighting abilities at the cost of causing him pain and an aversion to touching), so mages being horrible is literally all he knows of life before his escape. He has trouble adjusting to freedom, in part because his former master is still after him. He's illiterate, sucks at social interaction, justifiably paranoid, has trust issues, and often lets his temper get the better of him, for which he tends to apologize afterward. He also treats the mages in the party like crap; this is somewhat justified with Anders, as the story progresses, who is just as much of an ass, but he berates Merrill ceaselessly at the worst possible moments. Romancing him and helping him get over these issues is one of the many heartwarming moments in the game.
Isabela is a milder example, her irresponsible temperament and resistance to attachment are depressingly well-justified by the backstory she reveals if Hawke romances her.
Believe it or not, Jin Kisaragi from BlazBlue falls to this as well. He's a huge dick and can be called a disgrace to humanity in how he behaved. However, in the times when he was sane, he's actually a courteous man who seems to be ready to put his past as an Annoying Younger Sibling behind, until things from the past gets to him, and his Evil Weapon amplifies his emotions of the past, making him even more of a jerk than he usually is. There's also the fact that even when he worked his ass off to attain his position in NOL, his adopted family think that it's the family name that got him his position, making him feel like an outcast even in his own family. His "reincarnation" as Hakumen proves that, without said Evil Weapon, he can actually be a true hero, but still a jerk.
The main "protagonist", Ragna the Bloodedge, qualifies as well. Though he does have his good sidesand moments, he is for the most part rude, foul mouthed, verbally abusive and is perfectly willing to kill any and all innocent Punch Clock Villains that get in his way on his quest to bring down the NOL... In fact, it could be argued that the only thing keeping him from being an Anti-VillainProtagonist is the fact that 1) the realvillains in the BlazBlue-verse are MUCHworse than Ragna could EVER be, and 2) the most active of the Big Bads have seemingly made Ragna his designated victim, and has put lots of effort into fucking Ragna's life up as badly as possible. For example by possessing the earlier mentioned Jin, Ragna's little brother, and, through Jin, cutting off Ragna's right arm.
Travis Touchdown from No More Heroes and its sequel. He's a perverted fanboy who kills for money and enjoys it, but he's being conned the whole time and, when he finds out, genuinely feels bad about killing all those people for no real reason. His parents were also killed by his first love who, he later discovered, was his half-sister, who revealed that she had been molested on a regular basis by his father. Poor guy's trapped in an endless cycle of violence. No wonder he wanted to "find the exit".
The church guy. He locks you out of the safe room, and deliberately rings a bell to get the other survivors killed by a hoard of zombies, yet he's had such a rough time that you can't help but want to wrap him up in a blanket and give him a hug - especially as, at various times, he's almost sobbing his lines and obviously absolutely terrified. The poor guy also spends a lot of the time desperately trying to convince himself that he's immune. He's not.
Nessiah of Yggdra Union sits on the borderline between one of these and a Woobie, Destroyer of Worlds, and has a number of characteristics of both character types—he can be really, really manipulative and uncaring, but he is also seriously messed-up. Exactly what players perceive him as usually depends on how much they sympathize with him.
Xenogears is chock full of them. Ramsus & Hammer stand out the most. Xenosaga continues the tradition with characters like the tortured former serial killer/victim of government brainwashing/cultist/spy Cherenkov & Albedo, whose tragic life as a Tyke Bomb and agonizing over the thought of outliving his brothers turned him into the Ax-CrazyMemetic Molester we all know and love. There's also Virgil, a first-class Jerkass who keeps harassing Shion, but who watched the woman who loved him and saved his life get eaten alive.
DiZ, a.k.a. Ansem the Wise. He gets betrayed by his apprentices, whom he loved like family, and thrust into a realm of nothingness that drove him half-mad. In his desire for revenge against his apprentices, he becomes a Jerk Ass and does many morally questionable things, and in the end, is overcome by guilt once he realizes this. To atone, he makes a Heroic Sacrifice to save Kingdom Hearts from Xemnas. It doesn't kill him, but sends him to the realm of darkness, where he once again must endure a lonely period of banishment.
Axel may also count, particularly in 358/2 Days. As an emotionless Nobody, he's fundamentally self-centered, and eventually loses Roxas's trust, but it can be sad seeing him watch Roxas walk away, claiming that no one in the Organization would miss him and, in the Secret Report for Day 357, forgetting that Xion even existed as she dies. Then, of course, he tries to kill Roxas, and feels so bad about it later that he tries to bring Roxas back until, after realizing that this won't happen, he sacrifices himself so that Roxas's "true self", Sora, can succeed in his quest.
There's also, Ienzo/Zexion, No. VI in the Organization and the youngest of Ansem the Wise's six disciples. The "Woobie" comes from Birth by Sleep, where it's revealed that his parents were killed, with the now-orphaned (and noticeably withdrawn) Ienzo living as Ansem's adopted son. The "Jerkass" comes from banishing said father figure into the Realm of Nothingness after convincing him to continue experiments on the darkness in people's hearts and, later, attempting a Mind Screw on Riku in Chain of Memories. This makes his Alas, Poor Villain moment (which is perhaps one of the most brutal deaths of the Organization members; instead of a straight up death sequence, Re:COM reworked his final moments to have a Riku Replica suck out his lifeforce) even worse, as not only was his life horrendously tragic, but Zexion was seen to be unquestionably loyal to the Organization's cause (regardless of their actions).
Vexen in Chain of Memories, who, despite being an arrogant, twisted Mad Scientist, dies a horrible death at the hands of Axel (either literatelly stabbed in the back or burned alive depending on which version of the game you're playing) all while begging for mercy. Even Sora, who hated Vexen, is horrified and saddened by this.
Sa´x, given the glimpses we've seen of him and Axel in the past (as their Somebodies, Isa and Lea - seen in BbS), is another possible qualifier. And yes, he, too, had an Alas, Poor Villain moment.
Demyx is an infamous example. He's lazy, cowardly, funny, and would much rather play his sitar than do evil. Not a nice person, but not a mean one either. But when he finally gives in to his true, evil Nobody nature, he's killed by Sora, dying with a pitiful scream of "NO WAAAAAY!" and a sob.
To round out the above Organization XIII examples, the (albeit seldom canonical) novels implies that Larxene went through a particularly depressing number of troubles concerning the matters of the heart, which could explain her sadistic nature. And even in actual, undeniable canon, Larxene's death is played quite sadly. She's even played by Yuko Miyamura, who voiced the poster girl of this trope!
For that matter, once you hear his Final Speech, Psycho Mantis.
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.
Tales of Symphonia: Zelos Wilder. He's a jerk, pervert, and totally lazy, and betrays the group a few times, feeling the need to side with the side he thinks is the strongest. If you talk to him at Flanoir, however, you find out that he had to watch his mother die from an assassination attempt aimed at him. Her dying words were that he shouldn't have been born. He also says that his parents were forced together, which causes him grief. His people only see him as the Chosen and not as a person. If you choose Kratos's ending, Zelos betrays you, further solidifying his Jerkass status, but he also says, smiling the whole time, that he did it because Mithos promised to transfer the Chosen title to his sister. He also suggests that he's generally tired of living.
The manga adaptation delves further into his backstory to reveal his father abandoned him and committed suicide over an exposed affair when Zelos was a little kid, Cruxis recruited him when he was fourteen (because that's the perfect age to find out your whole life's been a lie) and dying was the end goal of his grand schemes because he felt everyone would be happier if he wasn't around. Ouch.
Luke starts out as selfish, ignorant brat and a megaJerkass, but right from the beginning you feel for him, because his memories of his childhood are completely gone, and since losing them, he hasn't left the manor. One moment he'll be obnoxiously blaming Tear for abducting him, the next he'll say in a horribly soft voice, "so that's what the sea looks like..." The Jerkass part becomes worse once he's named ambassador to Akzeriuth, but then the game breaks him over and over again, giving him a massive and justified inferiority complex and putting him through loads of horrible deaths, sacrifices and other traumas. By the time he offers his life to destroy the miasma, hearing him plead "I don't want to die!" is actually heartbreaking.
Asch is even more of an unrepentant Jerkass than Luke. He's unwavering in his cruelty to everyone, especially Luke, his replica. But he has an extremely justified reason for it, and when you learn that Luke basically stole his life in Baticul, including his childhood love interest, his hatred for Luke makes a lot of sense. He then spends the entire game trying to fix everything by himself, constantly fails due to circumstances beyond his control, and, of course, dies in the finale.
Jade is a milder version on both fronts; his Jerkassery is mostly limited to his occasionally extreme disregard for the sanctity of life and his near-constant snarking that borders on verbal abuse. His sense of timing is cringeworthy, and he'll often torment the others in his group even in their weakest moments. However, he has a very Dark and Troubled Past, and while he doesn't necessarily understand death or sympathy all that well, he tries desperately hard to do the right thing. Eventually, once he starts realizing the horrible consequences of inventing fomicry, he becomes increasingly miserable and repentant. It all culminates in an extremely heartwarming moment where, after declaring that the only way to stop the miasma is for Luke to pull a Heroic Sacrifice, he cracks and admits he doesn't want Luke to go through with it, because he considers him a friend. Aww.
Ganondorf in The Legend of Zelda: The Wind Waker, to a certain extent. Before that game, he was generally portrayed as a typical Evil Overlord. His speech before the final battle in Wind Waker, however, shows that his desire to conquer Hyrule stemmed from the awfully harsh life he had in the unforgiving desert. Any sympathy he gains from players, however, gets a little diluted when he subsequently proceeds to beat the crap out of Link in order to snatch the Triforce of Courage.
Scrapper from The Legend of Zelda: Skyward Sword is another example. He's generally very rude to Link, and unlike Midna, never really gets any nicer. However, he is the last remaining one of his species. The fact that he's blissfully unaware of this, though, may qualify him as a full on Jerk Ass.
LaCroix, the Camarilla Prince in Vampire: The Masquerade ľ Bloodlines. For all his ambition, ruthlessness, devious schemes, and the fact that he's the main antagonist in all but one of the possible endings, he's so damn ineffectual that he winds up coming off as more pathetic than villainous. Hell, unless you side with him, he doesn't get so much as a boss fight in the end. You just shrug off his attempt to dominate you and slice'n'stab him with a letter opener off his desk in a cutscene.
Doctor Zeppot from Dragon Quest VII isn't exactly a nice man, but his backstory as to why he's a jackass makes him oddly sympathetic.
In the Adam CadreInteractive Fiction work Varicella, the young king-to-be Charles is a sadistic, bratty, unlikeable powder keg as a result of his constant physical and sexual abuse from his "teacher", religious minister Bonfleche. Because everyone in the palace seems more concerned with grabbing power rather than addressing the unhealthy atmosphere within, Charles is eventually guided to becoming one of the most hellishly violent and ruthlessly competent kings of all time.
Fandral Staghelm is a racist who believes that night elves are the only true druids, is quite rude and patronizing toward players who do his quests, and, in Stormrage, works with the villain, helping to trap Malfurion in the Emerald Nightmare and trying to corrupt Teldrassil. It is, however, revealed that his wife died giving birth to their son and his son was brutally executed in front of him during the war of the Shifting Sands. Fandral's going astray is the result of seeing a hallucination of his son, and his mind is completely broken by essentially losing his son a second time. Even after being restored to some semblance of sanity after being brought to the Firelands, he's far enough over the Despair Event Horizon that he would rather destroy the world than live without his child.
Sylvanas Windrunner died a brutal death at the hands of Arthas during the invasion of Silvermoon before being raised as undead, and also lost many of her people to him. Even after being freed of the Lich King's control, she is uncertain what future awaits her, especially in the wake of the Lich King's defeat, and sees her existence as an undead as a form of torment. She is also incredibly ruthless to the Forsaken's enemies and tends to be fairly cold to those with whom she interacts. Sylvanas' woobification has grown to such tremendous levels that she's one of the Warcraft franchise's most notable example of a Draco in Leather Pants.
Varian Wrynn has a great deal of responsibility for the escalating Horde-Alliance tensions, and is hot-tempered and impulsive, often with many negative consequences. However, as a child, he lost his father to Garona and saw Stormwind overrun (influencing his negative view on the Horde), lost his wife to the Defias riots, and now has a strained relationship with his son Anduin, which motivates him to try to work on his temper and keep his Lo'Gosh persona in check. He may often make bad decisions, bud he has been through quite a bit, and while some of it is his fault, he has been motivated to change himself.
Genn Greymane, a grumpy old man by nature, walled his nation off from the Alliance after the Second War, abandoning them to the Scourge. In the years since then, his kingdom was attacked by the Worgen, he himself got bitten, and in Cataclysm, the Forsaken invade Gilneas, forcing him to swallow his pride and turn to the Alliance for help. To make matters worse, his son dies in that same invasion.
Jaina Proudmoore is heading toward this after Tides Of War and Patch 5.1. Her ruthless devotion to fighting the enemy, such as considering destroying Orgrimmar and expelling the Sunreavers from Dalaran gets her multiple What the Hell, Hero? speeches from neutrals and members of the Alliance, even hard-liners like Varian, and she often coldly brushes them off, sometimes while calling the people giving them cowards. However, not only did she lose her entire city, but she has had a history of fighting for peace, only to be let down or betrayed by virtually everyone else, making her bitterness understandable.
Sylvanas' sister, Alleria Windrunner, becomes this in Beyond the Dark Portal. She had to watch her homeland devastated in the Second War, during which her brother Lirath was killed by orcs. In response, she becomes obsessed with revenge and death, and becomes far more openly cruel towards others, including her lover Turalyon, which forms a rift between the two. As much of a jerk as she is, it's also apparent that her behavior, like that of many Jerkass Woobies, is also self-destructive, and her companions alternate between being upset at her actions and being worried that she'll ultimately get herself killed in her quest for vengeance. Thankfully, she comes to see her love for Turalyon as more important than her revenge, and gets off the path she's on.
Dante from Devil May Cry. He is constantly making snide remarks, complaining about money, extremely lazy (only works once a week), is in debt to all of his friends (and makes it clear that he won't be paying anyone back anytime soon), and is a major jerk to just about everyone. Then again, he consistently turns down payment (does the job anyway because it is the right thing) and refuses payment from the poor, saves the world on several occasions, takes care of Patty (to a certain extent), is shown to spare demons who are able to love and refuses to kill humans, and is shown to have a compassionate side as well as a kind side (he'll just give you a hard time).
His friends constantely take advantage of him (manipulating him, forcing him to pay for clothing, etc.), he is forever hunted and hated by the entire demon world (and most humans hate him because of his demon heritage), and he has no hope of ever having a normal day (let alone a normal life). During everyday life, he is constantly being shot at (Lady shoots him point blank through the forehead twice and later through the stomach...in a period of six hours!), impaled (a Running Gag to be stabbed through the chest or stomach), and other things. Capcom really wanted to make sure that Dante had the worst possible upbringing and life possible, didn't they?
The new Dante of the Continuity Reboot is even more of a Jerkass and somewhat more of a woobie. Reluctant to enter the fight for humanity and all around abrasive to enemy and friend alike, nevertheless he fights for whats right regardless of what it takes. He grew up without a family without his memories of them, fights demons that only he can see with powers he doesn't understand and everyone he kills looks human to normal people. At the end however he refuses to put the shoe on the other foot and subjucate humanity.
Portal 2 gives us Cave Johnson, the insane CEO of Aperture Science. He is a Bad Boss of the highest degree, and doesn't care very much what happens to his employees. Yet still, most of the things he and his company invented were by accident. He wanted to make a diet pudding, he made the propulsion and repulsion gels instead (a pair of gels that are definitely not to be consumed). He had a similar intention with the conversion gel too, and even tried it on himself...only to find out that it is deadly as all hell and works better as portal conductors. On a related note, he definitely spent more time testing his products than actually marketing them due to how horrible Aperture was at that particular task. This eventually leads to his downfall as he eventually goes bankrupt and, in his last moments, he uploaded his assistant's conciousness on to GLaDOS so that she would be able to run the facility in his place (despite the fact that she did not want to). In short, he would have been a millionare and an everyday hero if he had at least a little more sanity and some marketing ability, and the sense to use that ability.
Alma Wade from First Encounter Assault Recon. Sure, she's a psychotic Yandere that tries and succeeds at raping you, but she's also went through hell itself trying to save her children, and the flashbacks that we see of her past, where she's taken to the vault, are horrible.
The Origami Killer aka Scott Shelby in Heavy Rain gets abused by the hands of his father, along with his twin brother, John, tries to help him by getting their father, but refuses. This is how he becomes the villain that he is. His goal is to find a father who can give up his life to save his son. How does he do that? Kidnap the son and place the father through sadistic tests. If you played the level where it's the last one where Scott is playable, then you can have sympathy for him.
Herschell Biggs from L.A. Noire. He refuses to accept Cole as his partner after his affair with Elsa got out, but he begins to like him afterwards. It's just that during World War I, he has witnessed people burned and is close to retirement.
Giygas from the first Mother game is an alien that loved Maria and she cared for him. However, he was forced to kill her when his people ordered an attack as vengeance on George stealing their PSI information.
Liesolotte from Valkyrie Profile: Covenant of the Plume. you'll want to reach through the screen and hug her, telling her it'll be alright...then break her ribs when you see what she did to Rosea in the "A" and "B" paths. (Heck, even what she tried to do to you.)
To wit, the main source of conflict between the two is that they were expelled from the archmage's court because they were suspected of killing the archmage. Neither of them did it, all the know is that they didn't do it and think the other did it but saw their inability to own up as cowardice and this turned into hatred, resulting Rosea either stabbing Liesolotte, Liesolotte stabbing Rosea, or them stabbing each other to death. however, as it turns out, neither of them did it...it was Fauxnel - who even admits to doing it. Essentially, there's nothing they can do.
Sean "Sweet" Johnson from Grand Theft Auto: San Andreas. Yes, he is a gangster, who says, with pride in his voice, that he robbed people to finance his mother's operation. But all he wants is to build his gang on respect and loyalty rather than money, to keep his neighborhood dope-free and to wreak righteous vengeance on those who try to get his friends hooked on crack. He is betrayed by the people he trusted more than anyone and sent to prison, while said drug dealers run rampant in his absence, nearly sending him over the Despair Event Horizon. Oh, and both his mother and little brother were killed by drug dealers.
Niko Bellic in Grand Theft Auto IV, who had spend his early life growing up in the Yugoslav Wars and eventually becoming a criminal.
Trevor Phillips in Grand Theft Auto V, who was, apparently, abused by both parents (probably sexually by his mother), was permanently grounded from the Air Force because he was mentally unstable, met his best friend, Michael, started drifting away from Michael before he was apparently killed in a bank heist gone wrong, found out 10 years later that not only was Michael alive but living in the same state, meets up with him again, their relationship slowly frays more and more over the course of the game... and 2 of the 3 endings are downers for Trevor. In ending A, he's burned alive and is Killed Off for Real. In ending B, Franklin kills Michael, meaning his dearest friend is dead and one of the few people Trevor completely trusted betrayed him, and he cuts off all contact with Franklin. Of course, there's still one way to get Trevor a sort of happy ending, but when all of that shit's happened to you, it's really not that surprising that Trevor became a batshit insane meth dealer/addict and black market weapons peddler.
The eponymous Alan Wake of the video game, considering the situation he was in.
Cpt. Mark Bannon from World in Conflict. He seems like a Neidermeyer who always disobey orders from Col. Jeremiah Sawyer. This has led to the death of French Commandant Jean-Baptiste Sabatier, and the killing of many innocent Soviet civilians. But once you learn about his backstory, your opinion on him had changed. First, he had a telephone call with his step father. Then afterwards, his treatment by Sawyer. But by the end of the Cascade Falls mission, Bannon redeems himself by volunteering for a holding action against an overwhelming Soviet force. He apologizes to the Colonel before he, along with his company, perishes in the nuclear explosion.
While the fanbase is strongly split on her character, a decent number of Soul Calibur fans consider Tira to be this. Tira is a Psychopathic Woman-Child and Magnificent Bitch extraordinaire, but certain elements to her character besides her sadism and manipulation of others causes some people to feel for her a little, particularly the All There in the Manual expansion of where she came from. Tira was trained to be an assassin since birth; training that involved killing her mother figure at a young age and being treated like an object by the other members of her organization. After the assassin's guild she was in fell apart, she tried to live a normal life, but snapped and killed her family, deciding she couldn't live with normal people and devoting herself to Nightmare. While in-game she's mostly used as The Dragon and The Corrupter, there are some in-game hints that Tira is motivated not so much by sadism as by Undying Loyalty so that she doesn't have to be alone; even after all she's done, her ending in IV where she begs the dying Nightmare not to leave her alone is still a very humanizing moment.
A bigger example than even Tira is Aeon Calcos, also known as Lizardman. While he's served as a minor villain and by Soul Calibur 5 is a frightening man-eater with a case of Rage Against the Heavens, it's hard to find fault with why he hates the gods; he was a hero loyally fighting evil in Hephaestus's name before a rain of Soul Edge's power drove him temporarily insane and let priests of Ares turn him into a monster. Upon recovering his memories, Aeon is consumed with bitterness as he realizes his god abandoned him when he needed him the most, and is now caught between a man that wants revenge on the Jerk Ass Gods and his bestial side, which wants to eat people. What makes it worse is nobody knows or cares that Aeon was a good man before outside forces turned him into a monster.
In To the Moon, during The Stinger, it's implied that Neil might be dying, and depending on how you viewed his character, he can become this.
Final Fantasy X: Jecht. Later on in the game, he begin to see great strides of Character Development for this man. It's shown that Jecht, in his own way, genuinely loved Tidus, but could never properly express those feelings, so he tries to shape Tidus into a better and stronger man than he in his own way. This is further compounded when Jecht realizes that he'll never be able to return home. And as such, he decides to be Braska's Final Aeon, seeing it as a chance to finally be of some worth somewhere. Only this ends up backfiring, as due to the continuation of a 1000-year status quo, Yu Yuvon possesses Jecht and slowly reshaped him into the next Sin. It was all for naught! So, over the course of several years, Jecht was trapped in an And I Must Scream situation of almost unparalleled magnitude. It was only by luck that he and Auron were able to orchestrate the majority of the game's events, and even this plan was simply constructed so that Jecht could be felled by his own son.
Pretty much most of the Deimos cast in Arc the Lad: Twilight of the Spirits. The Deimos are pretty much social darwinists, finding nothing wrong with flat out murdering each other if it means they'll be stronger. This tends to lead to the Deimos characters' woobie-ish moments:
Darc is probably the biggest. He was half human and half Deimos. Unlike his brother, Kharg, was unable to hide that he is half human so he was considered a Deimos wannabe. His father dies, and he has to bury him himself. He is then taken in by Geedo and treated as a slave, and treated like crap by the local Orcon. He finally starts to get a friend in the form of Delma, and even gets her brother Densimo to help. Geedo sells him out to the Drakyr, his wings are ripped off, Delma tries to save Darc's life only to be double crossed by the Drakyr, Densimo eats the pyron that he and Delma kept safe from them...then everyone just taunts him and tries to have him killed for being weak. While anyone would want to hug him...they'd want to squeeze him a little too hard when they see how he acts towards humans...
Delma. Darc is probably her only friend, and he kills her brother. Rather than listen to him, she decides to kill him...but manages to get over her revenge spree.
Volk. He wants to do terrible things to Paulette to get revenge on her...but because she (And her father) killed his wife and son.
Camellia. She used to be young and beautiful, but was tortured and twisted by Tatjana.
And that's not to say the humans don't have their woobie-ish moments too, happily willing to engage in Fantastic Racism against Deimos.
Tatjana. Dilzweld essentially raises her, and when she manages to survive a Deimos attack, gets instead captured by the resistance and Dilzweld tosses her aside like a used tissue. The resistance will happily have her executed, and only the kindness of Kharg saves her from being sent to prison.
In the MMO "Wizard101," Necromancy professor Malistaire Drake, who, after going rogue and disappearing from Ravenwood, unleashes armies of Undead upon Wizard City, causes the Death School to fall into Nightside, allies himself with Meowiarty, the most dangerous crime boss in Marleybone in order to steal the dangerously powerful Krokonomicon, severely injures the Emperor of Mooshu in order to gain the Dragonspyre Spiral Key, and attempts to use the Krokonomicon to summon the uncontrollable power of Dragon Titan, who was responsible for the apocalypse of Dragonsypre, and would have been able to use the Krokonomicon to extend his reign of terror over the whole Spiral. It all seems pretty bad until you consider that Malistaire was deeply affected by the death of his beloved wife, Sylvia, and his only goal in all of this was to obtain the power to bring her back to life.
Subverted briefly when, just before the player battles him at the end of the original story line, Malistaire arrogantly expresses the belief that, as the Master of Death (essentially the most powerful Necromancer in the Spiral), he can control the Dragon Titan, even though the former Masters of Dragonspyre, who were presumably as powerful as him, could not. In other words, Malistaire has no qualms over causing havoc for Spiral, but does not wish to go so far as enslaving it under the Dragon Titan, although this would have been a direct result of the success of his plan.
Played straight again after the battle, when the defeated Malistaire, as a spirit, repents to the spirit of Sylvia, and to his living brother Cyrus, and joins Sylvia in the afterlife, as lovers for eternity.
Viconia from Baldur's Gate is a drow outcast who can be a huge jerk towards your companions, especially Aerie. She's often harassed herself, both before and during the event of the game, mostly because of her race rather than her attitude.
Odin Sphere's Ingway is a Manipulative Bastard who curses the man his sister loves with a Baleful Polymorph in order to keep the two of them apart, and who lies to, uses, backstabs and otherwise jerks around a substantial percentage of the rest of the game's cast in the service of his own personal goals. It's hard not to feel some sympathy for him, though, when you know his whole story: he and his twin sister Velvet were forced to renounce their mother and claim they didn't love her in order to avoid being executed along with her by their grandfather, and believe that she cursed them and died hating them for their betrayal. It turns out that Ingway caused the disaster that destroyed the entire country of Valentine by making the Crystallization Cauldron go out of control... which he did in order to keep his father, King Odin of Ragnanival, from being killed in battle against Valentine's superior forces, but the effect was much greater than he'd anticipated. To make matters worse, Odin promptly claimed the Cauldron without showing Ingway any trace of gratitude, affection, or compassion, instead dismissing him with a callous, "Well done, traitor," and leaving him to cope with the guilt of having wiped out his whole country for a man who wouldn't even acknowledge him as his son. His actions over the course of the game are one part trying to find a way to escape the curse of death that's on him, one part Calling the Old Man Out, and one part genuine but often misguided selflessness that backfires horribly about as often as it actually helps anything.
Soren in Fire Emblem Tellius. He's cold, harsh, brutally honest and with the exception of Ike regards everyone with indifference at best and contempt at worst. But he's also led one hell of a shitty life including Parental Abandonment, prejudice and physical beatings just for being who he is, not learning to speak until he was at least eight years old, and the one person who bothered to reach out to him disappeared and didn't remember him when they were reunited. First you want to slap him, then you want to give him a hug.
Zulf from Bastion is a pretty good candidate for jerkass woobie status. Sure, he goes berserk and tries to wreck the Bastion, sics his Ura kinsmen on The Kid and Rucks, and kidnaps Zia, but at the same time, he's also one of the sole survivors of a horrible cataclysm that wiped out most of the nation (including his fiancee) and gets rejected and brutally beaten by his own people at the climax of the game. He's sort of a destructive, treacherous bastard, but at the same time, it's hard not to take pity on him.
Juhani from the first Knights of the Old Republic game is a mild case. She grew up in terrible poverty and suffered from lots of Fantastic Racism on Taris after her parents became refugees from Cathar, which was bombarded in the Mandalorian Wars. Then her father became a drug addict and died in a bar fight. Then her mother starved herself to death so Juhani could eat, and Juhani was sold into slavery to pay her mother's debts, but thankfully a Jedi to whit, Revan saw the Force in her and freed her. Oh, and one of the first things to happen in the game is the destruction of Taris, meaning that Juhani's childhood home, however awful it was, is now gone. And then she had a terrifying brush with the dark side. However, she tends to be really defensive and snappish when you try to get her to open up about these things and has a case of Don't You Dare Pity Me! (although she does apologize for blowing up).
Severa from Fire Emblem Awakening. She's a Bratty Teenage Daughter to her parents, quite the Alpha Bitch towards the closest thing to a best friend she has, and can be incredibly harsh to anyone she crosses paths with. However, under that facade there's a terribly wounded girl who once seriously misjudged her mother out of fear and told her things she should have not said — and said mother died in battle before Severa could apologize, which wrecks the girl with guilt. Not to mention there's how her mother's fame has given her a massive inferiority complex, and how she and her friends are among the few survivors of one hellishBad Future. Now, can someone punch this girl to the ground, and then give her a bear hug?
There's also a particularly jerky and woobie-ish example in King Gangrel. He commits some true atrocities in the first part of the game, but it's possible to recruit him near the end, and if you do — boy does he have some Hidden Depths. You find him seeking out a living as a pawn for an abusive bandit chieftain, and he's long since realised how horrible he was during his time as The Caligula. He feels that he's crossed the Moral Event Horizon and can never be forgiven for what he's done, which drives him into crushing depression, though he tries to atone for his sins anyway. If you go through his supports, you find out that he started life with nothing, and when he took the throne he initially wanted to help his people before he allowed the power to corrupt him to the core. Worst of all, Chrom has been so deeply wounded by Gangrel's evil actions (which led to either the Heroic Suicide or the Trauma-Induced Amnesia of his beloved older sister Emmeryn, depending on whether you played her Paralogue or not), that he absolutely refuses to ever forgive him. And the person who can be either his best friend or his wife, The Avatar, isn't very convinced of his sincere intentions at first.
Clive Barker's Undying: The Covenants as a whole (excluding their parents) may fall into this category, but Aaron is probably the most unambiguous example: by all accounts he divided his time between doing nothing more sinister than painting pictures of Eternal Autumn and selling them to make a living and trying to keep Bethany away from the standing stones, and who was promptly horrifically tortured to death for his trouble, and who as a result had his spirit separated from his still-living-and-eternally-dying body to act out the Undying King's wishes. He's certainly not pleasant to deal with in-game, but most signs point to his being mostly innocent. Jeremiah may or may not count as well.
Agnes Crumplebottom from The Sims franchise. In the first game, she appears as an old spinster with very old-fashioned ideas of dating, hitting couples over the head with her purse if they showed any kind of affection in public. In The Sims 3, it's revealed that her husband died shortly after they got married, something she never really got over.