Naruto: many, if not most, of Naruto's opponents over the course of the series, notably:
Gaara of the Sand before Naruto beat the crap out of him. He kills people for looking at him the wrong way, but has grown up facing multiple attempts on his life from his own father, hearing that his uncle and mother, the two people he thought cared for him, never loved him or so he thought at the time. Naruto, upon hearing what he's been through, wonders if he's so much stronger because of how much he suffered.
Sasuke essentially struggled for his father's approval, only to lose his entire family in the Uchiha clan massacre. Then his brother proceeded to shove the concept of revenge down his throat while forcing him to replay the deaths of his family for three days straight, when he was EIGHT and again four years later.
Neji is introduced looking down on his teammate, Lee, and hating Hinata enough to Breaking Speech her about her inferiority and trying to kill her. It is later revealed that he believes that his father was killed for the main branch when he was young, and he can be punished at any time, potentially fatally, if the Main Branch members activate the Cursed Seal on his head. Once he learns the truth, he overcomes his previous belief that You Can't Fight Fate, which results in him working to improve his relations with the main family and getting along with Lee when he isn't acting too eccentrically.
Pain is responsible for many deaths, razed the Leaf Village and almost killed Hinata to teach Tsunade and Naruto lessons about pain, and is incredibly ruthless toward his goal of enforcing peace with tailed beast-based jutsu weapons, but his childhood was a long process of losing everyone he cared about and trying and failing to bring about peace.
Sora in the Fire Temple Filler arc, who is incredibly rude to most people, but has a dark past and an even darker present, as the host of much of the Nine-Tailed Fox's chakra.
Itachi Uchiha. He doomed himself to a life of being hated by his only remaining family, who he truly loved all along, along with the stigma of being a missing-nin AND part of an evil organisation, all while hating violence and combat. He was ordered to kill his family in order to prevent another war from breaking out, but he spared Sasuke. His actions were partly motivated by love for Sasuke, but he put on a cold emotionless front, acting like he just wanted to kill Sasuke and take his eyes (which wasn't true, of course); but one cannot deny that his methods of helping Sasuke (Mind Raping him twice) were a bit extreme. In short, you hate him for some of his actions, but once you learn the reason, you also want to hug him.
Karin. She used to be one of the most hated characters in the manga and she was a bit of a jerk before she started to genuinely care for her other teammates, but her being so badly hurt by Sasuke and her warning Sakura about Sasuke intending to kill her made her turn into a Jerk Ass Woobie for a good fraction of the fandom. Still, die-hard SasuSaku fans remain firmly in their Die for Our Ship position. The fact that she actually got over Sasuke after all he did to her has also helped pull her out of the Scrappy pile.
The Nine-Tailed Fox. You'd never believe it, but after the asskicking that it endured, to have its power taken from it and locked away again is very depressing. It openly expresses its bitterness over humans imprisoning it and using it as a power source for decades. This sentiment is starting to be recognized by the fandom. Even Naruto feels sorry for it, and apologizes for trapping it in its prison again.
Utakata, the Jinchūriki of the Six-Tailed Slug. He is quite aloof toward Hotaru and tries to rid himself of her at every opportunity, but this is largely the result of him being a fugitive for killing his master when he tried to extract his Tailed Beast, an experience that left him quite bitter and unwilling to trust others. And just when he comes to terms with this, Pain captures him and extracts the Six-Tails, killing him.
Manipulative Bastard Kabuto has become one. He had a deep existential crisis after Orochimaru's death (Naruto inspired him to continue) and he is shown thinking that all he wanted was for someone to notice him. He just wanted to be acknowledged. Still doesn't excuse his monstrous moral event horizon crossing moments though.
In the pilot, Naruto is even more of a brat than at his worst in canon, having no friends or social skills. He traps another youkai boy in a hole for bad-mouthing him, although it arguably edges on Kick the Son of a Bitch when the boy goes from insincerely claiming to be Naruto's friend to trying to blackmail him in a matter of seconds. And yet, when he's framed for murdering Takeshi, his horror and grief over the death of the man he was starting to befriend is heartwrenching. You also have to wonder what he went through when he is almost completely unable to understand why Kuroda would be willing to trust him enough to go to prison in his place.
Death Note have a portion of its cast packed with this kind of character.
Misa Amane. If she weren't so damn amoral, she'd be a very sympathetic character - what with her Parental Abandonment issues and her devotion to Light, which is both very crazy (seeing as how he doesn't really care about her at all and is merely using her as a pawn and eventually wants to kill her when she outlives her usefulness) and very genuine. She turns even more sympathetic when by the end of the anime, you learn she kills herself eventually.
Her live-action movie incarnation is even more of an example of this trope, as the death of her family is more focused upon (she mentions that she's fine with dying because "she should have died along with her family" when they were murdered, and she even keeps a picture of them in her room next to one of Light). The movie also shows that, if not for her insane fixation with Light, she could be a good person (she ends a killing spree out of hesitation when called a murderer, and later cries when she realizes that Light is willing to kill his own father.)
Misa in custody. Imagine the mental state of the poor girl. She's taken off the street, kept continuously blindfolded and restrained for two months, under constant surveillance, and she has no idea why she is there or if she will ever be untied. If she wasn't crazy before, she has every excuse to be afterward.
Mello, a mob boss that kidnaps innocent (and not-so-innocent) girls and a overbearing jerk that shouts at people but he acts that way out of a severe inferiority complex. He blows up his base, burns up his face, had Matt, his best friend killed by Takada's men, and dies horribly at the hands of Takada herself.
Beyond Birthday from Death Note:Another Note. L's neglected Backup turned Serial Killer. As much of a horrifying mass murderer he was, he was born with the ability to see when everyone is going to die, he was raised at an orphanage, neglected by his role model, and saw his classmate commit suicide (and knew it would happen). He's crazy and psychotic but ouch, he attempted to burn himself alive!
Teru Mikami. An Axe Crazy prosecutor who suffers from even greater Black and White Insanity than Light, he was a Bully Hunter as a kid and was mercilessly beaten for his efforts on a regular basis. His mother, a single parent, tried to talk him out of it out of concern for his well-being, making Mikami turn on her and actually rejoice when she was killed along with four bullies from his school in an accident. He unwittingly helpstrigger Light's downfall, and upon seeing his "God" for what he really is, falls into despair and dies in prison after the fact, at least in the manga. In the anime, he commits suicide right there on the spot by stabbing himself with his pen. Yeesh...
One Piece has Nami, the self-centered, mood swinging, thieving Insufferable Genius of the Straw Hat Pirates. However, her personality, in particular, her obsession with money, is explained as a result of being an orphan raised by the Marine officer Bellemere, along with another girl Nojiko. The family was too poor to afford the things Nami wanted, and when Arlong came along and imposed a tax on the people in her village, with the penalty for not paying as death, Bellemere only had enough money to pay for two; she chose to save her children rather than herself, and was shot in front of her children's eyes. Arlong then forced Nami to be a part of his crew, even going so far as to forcibly tattoo her, and said that if she manages to get 100 million belli, her village will be freed as well as herself. Even worse is that Arlong had no intention of keeping his end of the bargain, and wanted to enslave her for the rest of her life. Good thing she met Luffy and the other Ragtag Bunch of Misfits who dealt with Arlong personally.
Similarly, Boa Hancock was introduced as a puppy-kickingVain Sorceress. She showed herself to be an aloof, arrogant, complete Jerk Ass who wasn't above defenestrating her grandmother for giving the sincerest of warnings and petrifying her subjects for allowing a man (Monkey D. Luffy) onto their island. She was even complacent with her two younger sisters, Marigold and Sandersonia, breaking them in their petrified state just to mess with Luffy - just a hair's breath of crossing the Moral Event Horizon. However, when Luffy defeated the sisters and spared their pride by hiding their tattoos, this brought to light another side of Hancock unseen before: as she explained to Luffy, the tattoo was forced upon Hancock and her sisters (sensing a pattern here...), and is an eternal source of shame from slavery under the World Nobles, descendants of the founders of the World Government and, as shown in the previous arc, a whole 'nother ball of the MEH wax, known for kicking, shooting, and blowing up their slaves if they get frustrated or bored with them. The 3 sisters, who were just pre-teenage girls back then, spent 4 whole years enslaved to those bastards and were force-fed a Devil Fruit strictly for their entertainment. Hancock's own experience was such that she couldn't even talk about it without being reduced to tears. The very fact that she kept the law of her island to the letter could be explained due to her personal experience with one particular World Noble who was in her words "the very object of terror itself", which jaded her view on the opposite gender. It's only that Luffy didn't care that she and the other two were slaves, and hates the World Nobles anyway (for shooting a friend of his, who wasn't even one of their slaves) that caused her icy persona to warm up a bit, and even fall in love with the guy.
Kuina came off as rather arrogant and insulted Zoro a lot but she was covering up her huge self-esteem issues about her gender and being a swordswoman, being told that despite her talent, she will not be able to pursue being the best swordswoman in the world. Her father's suggestion that she might just have overcome her own limitations if she hadn't died makes her sudden and pointless death in an accident that much more tragic.
Shinn Asuka from Gundam SEED Destiny. Yes, he may be an abrasive jerk who needs to wake up and stop seeing the world in black and white, but during the story, he goes through such hell that you can't help but feel sorry for him. Especially considering how badly Sunrise and Fan Dumb abused him, coincidentally contributing to his total breakdown.
If you don't think that Fllay from the original Gundam SEED is The Scrappy, you'll see her as this. Yes, she's a Yandere who uses a particularly sensitive and troubled guy into almost killing himself for her sake as well as massively prejudiced towards Coordinators. But she's also pathologically lonely ever since she was a little girl, thrown into the middle of a war, watch her father die in front of her, AND she also sees the errors of her ways.
Once you get glimpses of their back-stories as Artificial Humans who were bred only to pilot Gundams, the Trinity siblings from Gundam 00 come off a pretty damn pitiful. Of course that does not excuse the heaps of shit they pull on everyone except for each other.
Even more so in the case of younger sister Nena, who is first left all alone as her brothers (who as mentioned above are the only persons she truly cares for) are killed in front of her, and later has to work with the guy who killed them in the first place. And then the karma she adquired for blowing up a wedding and crippling Louise catches with her. It's even better/worse/etc. when you learn through side materials that Nena actually spent more than half her Artificial Human life in stasis, and has only been conscious for seven years at the start of the series; that doesn't excuse her Psychopathic Womanchild traits, but surely explains why she has them in the first place.
Louise also falls into this - You can feel for her losing her family in front of her, but what she does during the second season can be seen as jerkassish.
Tieria Erde. At first, he's cold, stern and the most dedicated to Celestial Being's mission. However, after (thefirst) Lockon's death in season 1 and the separation from VEDA, we see that Tieria is a very insecure man.
Ranma Saotome has had a horrible childhood that, among other things, means that he has been inflicted with a Gender Bender curse that not only embarrasses him and frequently gets him into strife, but puts him at the risk of having to commit Seppuku at the hands of his good-hearted but Cloud Cuckoo LanderHot Mom — which means that he will not only die painfully, but die knowing that he disappointed his beloved mother so badly that she thought it would be best to die. He also routinely harasses his (admittedly, no saint herself) fiancÚe by hitting her where it hurts her the most (her relatively small chest [in comparison to his Gender Bender form and the rest of his fiancees]] and her inability to be properly feminine no matter how hard she tries) while being perfectly aware of how that's psychologically abusive to her, sometimes actively leads his fiancÚes on to satisfy his ego, and loves to harass and torment his rivals, despite knowing that they'll come after him with the aim of brutally thrashing him.
Ry˘ga Hibiki has terrible luck, is cursed to assume the form of a small, defenseless pig when he gets wet, has one of the worst ever seen cases of No Sense of Direction, the direction issues are inherited from both his parents and so he almost never sees his family, is a dedicated romantic, is too shy to even talk to other girls (despite the fact most would probably find him highly attractive), and the one girl he's in love with is engaged to someone else. He's also bad tempered and masquerade as her pet to get affection from her, even if it's only as her pet.
Mousse spins a heartbreaking tale of devotion and unrequited love that spans the better part of a decade, refusing to give up on his attempts to woo his childhood acquaintance no matter what blows life deals, to the point that an audience in-series cries after hearing it. However, the object of his affections makes it clear that he's more a Stalker with a Crush who happens to have been a childhood friend than the Unlucky Childhood Friend he sees himself as. There's also the fact that his response to the Love Triangle he's personally caught in as part of the Love Dodecahedron is to literally Murder the Hypotenuse, and as he has very poor vision, even with his glasses, and literally doesn't care who gets in the way...
Shampoo, particularly in the anime, genuinely loves and cares for Ranma, but gets little affection from him. Due to his Harmful to Minors training and a Baleful Polymorph curse inflicted on her as punishment early in the series, he actually runs away from her quite frequently. She's also a stranger in a strange land and has no friends at all outside of Ranma and Mousse (Akane might have counted as well if she and Shampoo had not been rivals in love). However, she's also coldly efficient to the point of being frighteningly amoral, perfectly willing to kill off someone she considers an enemy, and her preferred victims are the aforementioned Mousse and Akane, treating the first with incredible cruelty and being determined to get rid of the latter (And even Ranma has been appalled at how badly she treats them).
Uky˘ Kuonji is Ranma Saotome's Unlucky Childhood Friend, who felt so ashamed after Ranma apparently broke their Childhood Marriage Promise and stole her father's cart that she devoted her life to seeking revenge and even became a Wholesome Crossdresser because she felt that she was unworthy of being a woman. Even when she gives this up and tries to resume her courtship of Ranma, he not only does his best to avoid giving her any romantic favors at all, but he ruthlessly exploits her feelings. However, she is also quite willing to beat the hell out of any perceived rivals for his hand, slap Ranma around if he gets her flustered and upset, and team up with others (like Ryoga and Shampoo) to try to get the upper hand.
The Kun˘ siblings. Kodachi is just as willing as Shampoo to commit murder - she's just not QUITE as adept in combat; she has repeatedly used poisons on her personal ninja Sasuke as well as her own brother in an effort to master the art of chemical mind control. Speaking of her brother, (Tatewaki) Kun˘ only manages to not end up as a serial rapist in training by his status as a massive idiot with vaguely romantic pretentions (and by his attraction to girls that could mop the floor with him). They both pursue Ranma and/or Akane despite being pretty much the only ones in this entire series to be flat-out rejected. And then you find out that they, like pretty much everyone else in the series, suffer from Dead Mother Syndrome, their father returns from America after abandoning them for years out of an obsession with Hawaiian culture, and now they are both at risk of being attacked in their own home and getting shaved bald. Plus, he (their father) becomes the principal of his son's school, so Kun˘ can't even get a break during the day. And the anime adds in the sympathy by explaining that Kun˘ practically raised Kodachi in stead of their dad... which explains a LOT on how screwed up both of them are.
Ivan/Russia. A creepy, mentally unstable Stepford Smiler who has fun terrifying and abusing his subordinates, especially The Woobie, Lithuania...but his Despair Event Horizon/Start of Darkness is nothing short of heartbreaking, and he truly loves his Fragile Flower older sister, Ukraine, as much as his insanity lets him. You also can't help but feel sorry for him as he's constantly being pursued by his even crazier sister Belarus (also an example of this trope, as seen below), who wants to marry him. Also, Himaruya's new profile on him points out that he truly wants to have new friends. However it won't happen in a long time, because he's so scary that he ends up driving away potential friends.
Fanon sometimes interprets England as this, with him being quite ruthless and manipulative in his acquisition of his empire and family members and them eventually leaving him alone and lonely. Whether or not he actually is one in canon depends HIGHLY on your personal interpretation of his character, considering that the one who broke his heart the most was one he was shown to care very deeply for and take good care of in canon... which would make him a straight-up Woobie if not for how he also can show a rather bitchy, mood-swinging, and sometimes borderline childish behavior.
Japan sometimes gets this kind of interpretation too, from fans who believe that as ruthless and double-crossing as he may have been toward his siblings during his imperial period, he probably still did not deserve to have two atomic bombs dropped on him and may very well have become as emotionallybroken as his siblings in his misguidedpursuit of empire status.
Belarus, a terrifying Ax CrazyYandere became this when Russia threatened to send her to Siberia because Lithuania expressed reservations about accompanying him to a meeting. Can you imagine your own brother caring so little about you that he uses sending you to the horror that was the gulags as an incentive to make someone else do what he wants? If this happens on a regular basis, her bitterness comes as no surprise. Even if it's Belarus, that's just not right. There's also the fact that the poor girl is hopelessly and creepily but also very genuinely in love with Russia, her brother, who will never, ever return her feelings. The Jerk Ass part, specifically how she scares off anyone who is around her brother because she's jealous of them and how she once broke Lithuania's fingers on a date with him (the poor guy is such a sweet Nice Guy... but he refuses to see that Belarus not only is flawed, but that she does NOT owe him anything just because he likes her.)
The autor's notes also put her in this trope, explaining not only her Strange Girl behavior as well as what she's good at (gymnastics, fortune telling, etc.) but saying that she's always depressed and pessimisticdue to her history. It kinda puts her in a new perspective, though it doesn't exactly justify her bad behavior either.
Even though France is a lech, a liar and an all around bastard at times, he has his moment to be pitied. At the end of the first volume, there is a sketch of a much younger France with a girl with short hair and wearing armor. And she tells him, "I'm fighting for you, you know!" Yeah, she's Joan of Arc. We know how that ended. To think of France, hedonistic and arrogant, startled and then drawn to this one girl, only to lose her- it makes you feel for him at least a little, right? That's not counting the French Revolution, the Terror...on second thought, those pretty much explain (along with Jeanne's death) why France became the way he is. But that still does NOT erase how he flips skirts, gropes people without their consent, comes on them way too strongly on them for their comfort...
Lucia from Rave Master. The one that had to watch his mother die and got locked up for ten years for no reason when he was 6... but that still doesn't justify how he gleefully wanted to commit mass murder.
From Darker Than Black, Huangwas a cop until his best friend was horribly killed... by the woman Huang loved, who he discovered had just been using him to get to said best friend. He was left with no choice but to join the Syndicate or have his memories wiped, which he feels would be like killing his friend all over again. Tis resulted in Huang being a bigottedjerkass, all things considered.
Neon Genesis Evangelion: Asuka Langley Soryuu. Sure she seems like a total bitch, but she has an incredibly heartbreaking Freudian Excuse: When Asuka was very young, her mother, Kyoko, went insane and ceased to recognize her as her daughter. When Kyoko committed suicide, Asuka found her body, with the doll Kyoko believed to be her own daughter hanged right beside her, in a sort of would-be murder-suicide. Her father seemingly never cared about her mother in the first place, and began having an affair with the head nurse in charge of her. Her stepmother made it very clear that she disliked her and considered her an imposition. So far in her life, the people she cared about either a) killed themselves or b) revealed that they didn't care at all. Asuka threw herself into learning how to pilot EVA-02 in a desperate attempt to earn affection from others. She also feels that anyone she cares about will leave her, so she pretends not to care about anyone who she sees as weak.And then the events of the series kicked in. Including the Trope Namer for Mind Rape.
In End of Evangelion, she finally gets to see her mother inside Unit 02 and feel love and acceptance from her...only to be shortly thereafter forced through the experience of being eaten alive by the Mass Production Evas.
One of the later episodes features Asuka naked, hollow-cheeked, and lying in a tub, well past the Despair Event Horizon, stating that she no longer has the will to live. The tub appears to be filled with a red liquid indicating that she tried to kill herself by slitting her wrists. Poor Asuka...
Impmon/Beelzemon from Digimon Tamers. He starts out as The Imp, but later, his human-hating tendencies are explained by the fact that he was fought over by his toddler Tamers, getting physically hurt. But it's not until he, unable to digivolve by traditional means, makes a rather shady deal with Chatsuramon, one of the Devas, that his true jerkass side shows. Of course, in order to be able to evolve, he has to kill the Tamers and their partners. He honors his deal by killing and absorbing Leomon.He deserved a punch on the face. Also, a big hug.
Yukio Oikawa from Digimon Adventure 02. Growing up as a lonely boy in a unforgiving world, the only friend he ever had was Cody Kida's father. During their youth, they became the very first humans ever to discover the Digital World, and they together promised that they would one day travel to it. Of course, fate decided to be a mean bitch one day and killed off Hida during his line of duty as a police officer before it could happen, leaving Oikawa with no one else in the world but his promise. Depressed and lonely, he became a easy target for Myotismon's ghost to possess, who promised him that he would help him to get to the Digital World and fullfill his promise to Hida...at the expense of everything and everyone else.
Gatomon from Digimon Adventure, being the willing servant of a wannabe Multiversal Conqueror, sarcastic, ruthless, disparaging people, and smacking dogs. Then we learn that she was tormented and enslaved by her Bad Boss, but it doesn't make up for the fact she is callous. Then shortly afterwards, she discovers her true self, pulls a Heel Face Turn, and becomes an non-jerkass Woobie.
Kyo to a lesser extent. While not as bad as Akito in terms of Jerk Assery, he still came across as an asshole to everyone in the first few episodes. But then again, would you be a nice guy if you were the family outcast, your mother committed suicide because of you, your father resented you because of said suicide, and then got Tohru's mother, a woman who acted very motherly towards you, killed (not intentionally, mind you) because you'd risk exposing your secret?
A large portion of the cast of Code Geass not only do nominally immoral things for their cause, but also find themselves treating others poorly when it's obvious that either that's not what they really want to do, or they're too far gone to really do anything: Lelouch, Suzaku, Kallen, C.C., Rolo, The Emperor, Marianne, Guilford...
Seto Kaiba, though less so in the anime adaptation, where he stays a jerk long after the finale of the Battle City arc, which, in the manga, was supposed to be where he let go of his tragic past and became a better person.
Pegasus and Marik also fit this trope, what with their heartbreaking tragic pasts.
Also Aki of 5Ds. Yes, she was ostracised as a child by her parents for having magic powers, and subsequently found by a lunatic who wants to rule the world for no adequately explained reason other than "I'm different and therefore I should be on top of the world". But that smile she wore when using her magic powers when dueling, especially against Yusei, was damn creepy.
Hansel and Gretel. It gets easy to see why they were Ax Crazy all the time and at least feel sorry for them. Then, after Balalaika gives Hansel a Shut Up, Hannibal! treatment as punishment for harming the subordinates she's so protective of, she orders her men to blow his hand and leg off. When he's lying there, crying and bleeding to death, it's easy to forget that he was a mass murderer. This is taken to further extremes with his sister Gretel, who states that she always wanted to see the ocean and has a heartbreaking Evil Cannot Comprehend Good moment when Rock offers her kindness and even sheds tears for her. When they finally reach a seaport and her wish is granted, she has her brains blown out by an assassin hired by Hotel Moscow, as Laser-Guided Karma for what she and Hansel did to the persons under the lead of the next one in line....
Sofiya Irininskaya Pavlovena, alias Balalaika. Thanks to the Afghan War, the girl who Used to Be a Sweet Kid and wanted to become an olympic sniper ended up as a cynical, stylishly brutal Mafia queen and cold-hearted MagnificentBitch. She's also quite the Mama Bear who shows no mercy to anyone who harms her subordinates, which proves that she's still human: those men are all she has anymore, so she protects them fiercely. And yes, she's the one who has both Hansel and Gretel horribly killed. Because they killed a subordinate and tortured another to death.
Kanda Yu turns out to have a very good reason for being so cynical and rude to nearly everyone. Namely, this, over and over again for months. Additionally, he was created artificially and knows it, grew up with very little human affection, and was eventually forced to kill his only friend, who had gone berserk and killed 40-some people. Also, the Second Exorcist project, which Kanda is a product of, involved implanting the brains of dead Exorcists into new bodies, and he eventually started regaining memories of his own death. Kanda's life sucks so much that using an Exposition Beam to show someone his memories qualifies as Mind Rape, and the local Creepy Childfeels sick when she sees them.
If you don't feel bad for Kanda after seeing this, you're a horrible person.
Kaede from Shuffle. You feel bad for her for how messed up in the head she became following her mother's death and how she lost the will to live. But you also hate her for treating Rin like shit all throughout their childhood, because he decided to take the blame on himself so she wouldn't figure out that the death of her mother was actually her fault. For what it's worth, when she finds out the truth, she ends up hating herself for how she treated Rin and decides to try to atone for her bad actions by devoting herself to Rin. Rin does not really want this, but he is afraid of making Kaede have a relapse by not allowing her to punish herself in this way. Kaede is also shown to have romantic feelings for Rin, but considers herself unworthy to be loved by Rin or to stay by Rin's side, and acts like a Yandere (in the anime) when she finds out he and Asa are a couple, as she completely loses her self-worth at the sight. There's also the fact that Kaede has feelings for Rin and is hopelessly devoted to him, but Rin is Asa's boyfriend, so Rin simply cannot never return Kaede's feelings.
Akira Inugami from Wolf Guy - Wolfen Crest. He rescues his Morality Pet teacher from baddies regularly, gives hope to his oppressed fellow classmates, and stops an Ax Crazy psycho from gunning down the student body vice president at point-blank range, but he can be a cold-hearted snarky jerk to everyone. He also lost his parents at a very young age, has a habit of making enemies who want to violently beat him up and murder him, and is pursued and lusted after by twoAx Crazy psychos who are major threats to anyone he is close to or not. Basically, he's a nice guy underneath it all, but he spares NO ONE the snark and is literally the unluckiest bastard walking. Which backfires horribly when his beloved teacher becomes his Morality Chain — and one of the Ax Crazy psychos has her kidnapped and gangraped. Which causes Inugami a heartbreaking Heroic BSOD.
Rosine, the Big Bad of the Lost Children arc, qualifies because of the horrible home situation that drove her to become an Apostle, and her yearning for elves to be real. Though she and her "children" commit a number of acts that should make her cross the Moral Event Horizon like many of Berserk's other villains, she comes across instead as a misguided, emotionally damaged little girl who just wanted a little happiness that she couldn't find at home.
Souma and Sakurako Saiki from Sakura Gari. Initially, it seems as if It's All About Me with them, and they'll do whatever it takes to get what they want even if they hurt/kill others in the process. Also, every one of Souma's lovers are shown to have horrible endings. He even notices and mentions it himself. Of course, this doesn't stop him from continuing to take lovers. However, even with all their flaws, it doesn't make their backstories and endings any less heartbreaking or messed up. And at the end, due to his actions, Souma ends up driving away Masataka, who he had genuinely fallen in love with, and, in the last panel, he is shown crying into one of Masataka's shirts. And as for Sakurako, we find out that she's actually a boy named Youya, desperately lonely and unstable after his/her mind totally breaks when s/he was a child, and s/he ends up commiting suicide when s/he thinks s/he's killed Souma... not before having a heartbreaking Villainous Breakdown where s/he attacks his/her dad while asking "why I was born? why was I brought into this world?!".
And Break. Sure, he's not always nice, and it's not obvious that he's a Jerk with a Heart of Gold, but he does have his moments. In the past, it's revealed that he signed an illegal contract to try to change the fact that the family he was bound to protect was betrayed and massacred. Then, he was dragged into the Abyss and had his eye torn out, only to have the family die off anyway. Currently, he's going blind in his remaining eye.
Leo too. He becomes crazy and lonely after Elliot's death and becomes more of a jerk. He feels like Elliot's misfortune and death are all his fault.
It's likely that one feels sorry for Greed at one point of the series too...or while reading chapter 107 at the least.
Envy pushes the Jerkass side of this almost to the breaking point. On the one hand, he crosses the Moral Event Horizon repeatedly and is absolutely gleeful about it. On the other hand, his death makes it obvious that he's incredibly jealous of human concepts like compassion, friendship and empathy, and when you realize what that says about the homunculus family dymanic... yeah.
S˘suke Sagara. Originally a sweet, innocent kid, his heartbreaking backstory turns him into a cold-hearted Jerkass. He finds it extremely hard to understand other people's feelings, and tends to do very morally ambiguous things without much consideration for others. Most of the time, it's played for laughs. There are numerous times where he finds himself unable to understand why someone feels fear or sadness (even when someone died). The poor guy goes through so much crap throughout the series, though, including his childhood as a child soldier, so it's easy to feel sympathy for him despite his flaws.
Xia Yu Fan and Xia Yu Lan. Out of all the villains, these two seem to garner a lot of sympathy among fans. The fact that they were taken in by Gauron of all people at such a young age certainly deserves sympathy.
Hitagi Senjougahara. She acts cold and abusive towards others, especially towards her eventual boyfriend, Koyomi Araragi. She also pulls out a stapler and a box cutter, threatens Koyomi with them by shoving them in his face, and promises to disfigure him with them if he reveals her secret, then uses them anyway (stapling his face as a warning). All this within minutes of the start of the first episode. In episode two, Hitagi recounts how her mother joined a cult when Hitagi was sick, and that one night, her mother brought a higher up from the cult home. Hitagi injured him as he attempted to sexually assault her, while her mother watching without aiding her. As a result, her family was broken apart with Hitagi feeling that she's responsible. After that, she met a crab which took her feelings(weight) and memories of her mother. Hitagi begs the head crab to return to her the lost memories of her mother and her feelings(weight), but despite this, she has forever lost her mother.
Mayoi Hachifuji. She knows that she is caught in or actually is a supernatural event and doesn't want anyone else to have to get involved. She's a 'snail,' otherwise known as a spirit that distracts people who are avoiding going somewhere and makes them follow her. She knows that she's dead and won't reach her destination, so she tells anyone who talks to her that she hates them so they'll leave her alone and not waste their time on her.
Mugen is a crazy, Badass, insane Anti-Hero whose childhood makes anyone want to cry...
Jerkass may be a strong word, but Fuu fits as well. She's often temperamental, unappreciative of her bodyguards (to be fair, they do abandon her a few times), and seems to recklessly search for someone with almost no leads. But like Mugen, she's also lonely and her search for the sunflower samurai turns out to be because he's her dad, and he abandoned her now dead mother to save her and Fuu from being persecuted by the anti-Christian government.
Gilbert. He may be antagonistic and even violent toward Serge (especially in the beginning), but he sure went through a lot of crap in his life...
While he doesn't hold a candle to Gilbert when it comes to sheer woobiness, Arion RosemarinÚ nonetheless qualifies once certain aspects of his past come to light. Yes, he's ill-tempered and physically abusive (particularly towards Gilbert himself) but he's also rather pitiable in his own right... specially when you learn he was physically and sexually abused in his past.
Nagi somehow manages to earn the love and sympathy of the audience in spite of being a self-centered little brat. Maybe it's her adorably innocent Cry Cute moments.
Although Nagi has outgrown the self-centeredness, Athena seems to have taken her spot. She harshly taught Hayate for her own gain, but has had moments when you can't help but feel sympathy for her.
Louise of Zero No Tsukaima. Saito too. His pervertedness can be too much at times, and he sometimes pokes fun at Louise when she's just minding her own business but Louise frequently beats and berates him, sometimes to Heroic Comedic Sociopath levels, and Saito's stuck in an alternate world (though he decides to stay after falling in love with Louise). And he tends to go all out when trying to protect Louise or his friends from harm. His selfless heroic side tends to be immediately followed by him demonstrating his idiotic perverted side, though. It's also later shown that Louise is constantly being pressured by her family to get married and she's frequently bullied by one of her older sisters who has a bigger temper than Louise. Oh, and although Louise is in her second year at the Tristain Academy of Magic, her magic skills still need a lot of work. Because of this, she lacks self confidence, and her classmates look down on her, calling her "Louise the Zero", frequently teasing her for her zero success rate and flat chest (including Saito!). This gets worse because most of the female cast except her (and Tabitha) are busty. And Saito's total lack of proper human interaction is pretty clear - he knows nothing about sympathy (remember, Saito Ś when someone's crying, it means something's wrong), empathy (his total inability to figure out how to not piss someone off), and sincerity (telling Louise he loves her while fantasizing about her sister), but despite his flaws, he truly does care for Louise, as shown by his willingness to take her beatings and almost die for her.
Saito was kidnapped from his world, treated sub-humanly, made into a slave for a bratty, over-privileged little girl, and had his mind screwed with magically (though he doesn't know it).
Muramasa. Sure, he personally instigated the Zanpakuto Rebellion and incinerated Katen Kyokotsu and Sogyo no Kotowari to death, but as Kouga descended deeper into madness, he quickly became a self-centered, arrogant, abusiveJerk Ass that frequently treated Muramasa as a mere tool, instead of an actual person. However, since Muramasa was the one that led Kouga to his crazy, power-drunken self, one could say that he brought it on himself. This disharmony caused Muramasa to literally lose the ability to hear his master when needed...which led to Kouga stabbing Muramasa as soon as he was unsealed, completely uncaring about Muramasa's explanation.
Also, Homura from the third movie. There's no denying that Homura was a stubborn, jealous, possessive, and irrational teenage girl, who had the potential to be as unstable as Loly can get at times, with an almost-unhealthy obsession towards Rukia to top it all off; but for all her faults, she was a sincerely sweet and cheerful girl, whose only wish was to reunite with the only other friend and loved one she had. In fact, she wasn't even evil to begin with, just selfish, naive, and misguided, with a justifiable excuse for her implied hatred (and fear) of the Shinigami. Considering her past, her interactions with Rukia are all the more heartwarming; as an orphan, she was forced to survive on her own in a lawless slum district, ended up getting murdered by an (albeit mind-controlled) Shinigami, absorbed said mind-controlling hollow into herself as a fail-safe to keep it from killing Rukia (thereby making it into the subconscious source of her power), and unintentionally causing the now-innate hollow spirit energy to revive and transport them to Hueco Mundo, where she presumably spent most of her life relentlessly fighting for survival against hundreds of cannibalistic monsters in a dimension she knew nothing about after forcing the still-barely alive hollow into submission. And keep in mind that, at the time, she was barely over the age of ten. The final kicker is that Homura was a genuinely likable and sympathetic character, even taking into account her Yandere/Psycho Lesbian tendencies, which makes her death scene even more of a Tear Jerker than it already is.
The arrancar Ulquiorra. He's stated to be the personification of Nihilism, is loyal to Aizen, considers Ichigo and all others below his power level little more than "trash", helps Yammy to kill Tatsuki's judo classmates, cannot comprehend things like love and friendship, kidnaps Orihime and verbally/psychologically abusive to several degreess towards her, physically mutilates her friend Ishida, and kills Ichigo in front of Orihime merely to prove a point to her, then taunts her until she massively breaks down. However, he seems to gradually soften up towards humanity thanks to his interactions with the captive Orihime, and Ichigo, too, to a lesser extent. He also regards the senseless killing done by other arrancars as childish, and is disgusted when Nnoitra says that he should rape Orihime. His death is also incredibly heartbreaking. It even seems like he is finally starting to understand human bonds, seeing how, in his last moments, Ulquiorra reaches out to Orihime and asks her if she finds him frightening, mirroring their conversation before Ichigo arrives in the tower. She replies with tears in her eyes that she doesn't and reaches back for him, but his body dissolves before they can touch. Of course, however, fans go from considering him a Jerk Ass Woobie to something else entirely.
There's also Kaname Tousen, the only Captain to ever gets The Scrappy status, who betrays Soul Society for a hypocritical reason (going down the path with the least bloodshed by joining the Big Bad). His close friend was killed by her shinigami husband, after she scolded him for killing his comrade in battle. So, he joins up with Aizen, pretty much wants all the shinigami dead, and is willing to destroy a town full of people, all to get revenge on every single shinigami. After being beaten by his vice captain and being reminded of his errors by his best friend, Tousen seems to repent, cries, and wants to have one tender moment with his vice captain...and then blew up in front of his vice captain and best friend.
Hiyori Sarugaki, an aggressive and short-tempered girl with rather violent tendencies who seems to hate everyone around her. However, many fans felt sorry for her when Hollowfied Ichigo tried to strangle her to death and Gin cut her in half, as well as the part where she gets turned into a Visored in the first place. She also shows a more vulnerable side at times, such as when she confesses to Shinji that she hates humans and Soul Reapers.
Cirucci Sanderwicci is a rude and cocky bitch. Still, she's not all bitchy; in one specific scene, she does garner sympathy after losing her powers by showing a rather dignified sort of anger at her defeat, and generally showing Villainous Valor and a thoughtful attitude during her fight against Ishida.
Jackie Tristan of the mysterious organization Xcution. She tries to kill Renji and ends up dead instead, and Chapter 471 features her returning home with her dead brother in her arms to find her entire family slaughtered, which is the reason why she want with the Fullbringers in the first place.
Yukio. His sadism might've been biological, but he would've been far less homicidal if his parents gave enough of a damn to raise him properly. Fully explained in chapter 471: he was a former Cute Mute who was kept locked away by his parents due to his speech impediment, and was so lonely that he first used his powers to recreate images of his parents as sort-of Imaginary Friends.
For some, that would be Loly. Yes, she's a massive bitch and treats Orihime like crap, but it doesn't necessarily mean she exactly deserves to be mutilated by Grimmjow and later mauled by Yammy to almost death. A few also feel for Menoly, too, since her primary problem is that she follows Loly loyally in spite of her own doubts.
Ichise of Texhnolyze. He's rather Stoic and cold to nearly everyone (which includes not even saying "Thank You" to one guy who was kind enough to give him a meal when he was starving), and he's even like that during his youth: when he was younger, he found his dead father hanging from the ceiling, and while his mother cried at the sight, he showed little emotion and was surprised by his mother's reaction. He also has a tendency to have violent outbursts and gives the Death Glare to people who annoy him. However, practically the whole anime puts him through an extreme Break the Cutie cycle which includes both parents being killed, growing up as an ostracized outsider, working as a fighter in an underground ring, having two of his limbs cut off as punishment for using his fists to defend himself against a sadistic woman, has to go through the agonising pain of learning how to use new artificial limbs, watches his entire world deteriorate, gets beat up to a brutal degree, gets thrown down a sewer, nearly has his remaining limbs cut off, realizes that the entire human race is effectively dead, and then watches the only human he actually has a connection with have her head stuck on the body of his enemy. To top it all off, he dies in the last episode.
Edmond (or The Count of Monte Cristo) from Gankutsuou.
Genkaku from Deadman Wonderland is an asshole-ish psychopath who makes Nagi's life a living hell. He's later shown to have been a timid, cute monk that got repeatedly beaten and raped by bullies in the past, with the elder monk in charge being unsympathetic and uncaring, and seeing the little wounded kitten he was taking care of die — all of this causing him to go insane. Considering what happened to Genkaku...you really understand how he became the Ax Crazy psychopath he is, and you can't help but feel sorry for him, especially when he ends up dying with Nagi.
Eva Heinemann in Monster. Terrible, psychotic Rich BitchWoman Scorned... who still doesn't deserve what happens to her and her beloved bodyguard, Martin.
Harry MacDoogal from Outlaw Star. Yes, he's a villain, and an Ax CrazyStalker with a Crush at that, but when Hazanko destroys him, Melfina cries out for him, and when he appears as a mechanical "phantom" before Gene and Khan and helps to open the door, his final moments are so poignant that you almost wish it didn't have to end that way. Also, you got to feel sorry for him because he has feelings for Melfina and she doesn't share the same feelings for him and he does everything he can to make her love him only to fail and get curb stomped by a massive douchebag with the ability to break his body parts like a bendy straw.
Nanami Kiryuu. Good lord, what a bad day she has had... After discovering that her brother Touga, who she loved ever since she was a child, was not her blood sibling, she feels like the connection she had was fake, and now has nothing to hold on to. After that, she runs away from home, into the house of a pair of close, happy siblings, only to walk in on them having sex. And after that, she walks in on Touga making out with a member of her old gang, to hear her brother say that he never loved her to begin with, and to have her ex-friend claim that she has no connection to her anymore. And then after that, she gets the Akio Car treatment, where Touga attempts to rape her, which she fights off in fright, and then loses her duel, sobbing that she feels like she's just a face in the crowd and has no way to reconnect with the brother she loves. It's very hard not to feel sorry for her after all that, even though she was a raging Alpha BitchYandere most of the time. She does seem to become nicer afterwards, too, warning Utena to not hang around with Akio or Anthy anymore as she thinks they're up to no good, but her warnings fall in deaf ears. Ouch.
Mikage Souji could qualify as well. Just as he was beginning to evolve out of his computer-like personality and developed feelings for a woman named Tokiko, Akio seduced her just so he could manipulate Mikage into burning down the memorial center. And, of course, killing the 100 boys trapped inside. Not only that, but Akio gets Mikage to work for him years later as a puppetmaster, pulling the strings of the black rose duellists. Unfortunately, Mikage doesn't know that he's a puppet at all, and that Akio has tampered with his memories.
Saionji too. Yes, Saionji was a total Jerk Ass, but not even he deserved Touga's horrible treatment and manipulation of him.
In the Watanagashi/Meakashi-hen arcs, Shion Sonozaki pretty much fits the bill. On the one hand, there's everything that she has had to go through as The Unfavourite of her family, never mind the Cold-Blooded Torture she's put through just before she finds out about her boyfriend Satoshi's disappearance — which she had gone through specifically in order to prevent. On the other hand, her Roaring Rampage of Revenge goes so far off the rails (specially in the case of Satoko, whom she straps to a cross and tortures to death, and Mion, whom she forces to watch as she murders poor Satoko) that it's hard not to be relieved when she finally gets her Karmic Death near the end, if only for her own sake.
Nakai of Bakuman。. While he crosses the Moral Event Horizon in the eyes of the readers and some of the cast when, after seemingly getting Kato's attention, he asks Aoki to be his girlfriend in order to have him draw for her, Then there's his whiny-ness, he essentially has the same dream as Moritaka (getting a girlfriend and a manga series), but has been at it for longer and has not had nearly as much success.
Ebisu typically exhibits both aspects of the Jerkass Woobie simultaneously, rather than appearing to be a jerk with a more sympathetic side. In the past, he lived without parents, and supported himself by commiting petty crimes with his skills as a medium. When a ghost turned on him, he got saved by Goryo, and became his assistant in his Magical Law business, which had become ruthless in the way it did business. He's typically fairly arrogant and condescending towards most people besides Goryo, but at the same time, comes off as pitiable after being fired for failing to execute one of Goryo's plans, even if he eventually gets back together with Goryo. He never completely changes and doesn't regret his actions, even if he acknowledges that many of them are less than noble, but his past shows that he mainly does what he does out of loyalty, and he helps to teach Roji a lesson about how he can best help Muhyo.
The Cortlaw siblings are this to varying degrees, with Mick being the heaviest on the Jerk Ass end (killing Panza when she tries Taking the Bullet for Roji) until his final moments, Ivy a mixture of both, and Kid being mostly a standard Woobie complicit in Ark's plans (albeit largely through manipulation with a few critical lies). They lost their parents to the MLS (unaware that they resisted arrest and killed some of those sent after them) and are willing to resort to dark magic to bring them back. Kid admitting he was wrong and hoping to see his family again as he is dying is particularly heart-wrenching.
George Schyuter keeps Muhyo and Roji out of the investigation largely out of pride and the belief that they're unable to help, and even puts a sword to Roji's throat when he tries to help. It turns out, however, that his attitude and belief in working alone was the result of losing all of his partners and being blamed for it. He found a way to practice Magical Law alone, but derived no satisfaction from it, since no one was with him to share his defeats or victories.
Arguably, Haruhi Suzumiya. She learns, rather painfully, that she isn't all that special, and in her quest to make her life special, goes on a hunt for aliens, time travellers, and ESPers after some inspiration from Kyon. This leads to her general sociopathy and her obsession with cosplaying Mikuru. Kyon says that, through her Character Development, she's not exactly turning into a good person, but is returning to be the kind kid she once used to be.
Ayato Naoi of Angel Beats!. He's kind of a Jerkass to everyone, except Otonashi, but when alive, his brother was his father's apprentice in pottery, while he remained in his room, ignored by the world. Then his brother died and he had to take his place, but wasn't nearly as good at the craft as his brother. Having no choice but to live his life as someone else, he began to think that his entire life was a charade.
Kevin of Karate Shoukoushi Kohinata Minoru is established as one of these in chapter 66, when it's revealed that he was abused by his mother after she remarried and began to favor her stepchildren over him.
Kuromi from Onegai My Melody may qualify, giving that the reason why she's acting like a jerk is because My Melody made her life miserable.
Vita was used as a personal soldier for the owners of an Artifact of Doom for centuries, and seemed to take it harder than the other Wolkenritter. While doing so, she was also quite abrasive to her allies, especially Reinforce, pushing them away when they tried to get close to her, and showed cruelty to her enemies beyond what was necessary to collect their Linker Cores. She becomes a nicer person after meeting Hayate, but still is not above barbs about the size of Signum's breasts and the lethality of Shamal's cooking.
The Huckebeins from Force. They're afflicted with a deadly virus that will kill them unless they kill other people, and have resolved to do what they have to to stay alive. Okay, fine, villainous but understandable...what isn't is the degreeof dickishness with which they go about it. The fact that they've been immune to karma so far doesn't help matters.
Precia in the first movie. She's just as cruel to Fate as in canon, but it's revealed that not only was she a loving mother who wanted to spend more time with her daughter, but she tried to prevent the premature launch of the reactor that caused the meltdown that killed Alicia, and the companion manga shows just how painful it was for her, especially with her cradling Alicia's lifeless body in her arms as tears are streaming down her face. In her final moments, as she's falling to her apparent death, she appears to finally understand Alicia's desire for a little sister and regret her actions.
Also from the anime, Meowth. He's technically a mafia goon and kind of a jerk...but that's because he grew up an alley cat on the streets and worked his tail off learning to speak human to impress a girl-cat, only to be rejected and ostracized as a "freak". He ended up as a goon in a criminal syndicate because it was the only place he could find that would have him.
Kyouko Sakura. She's introduced as an amoral, Ax Crazy, borderline evil Dark Action Girl... and then we learn that her family was destitute after her minister father was excommunicated, she used her Wish to get him followers...and when Dad found out, he went mad and killed the whole Sakura family except for her. It certainly helps that the person she mocked the most, Sayaka, was also the one who unlocked her Hidden Heart of Gold.
Homura, too. She first appears in the act of severely injuring the series's lovable mascot (in fact, she had already killed him, but he revived himself, so she was trying to kill him again). Later, she gives vague, threat-like warnings to Madoka, and generally acts creepy and ominous. She doesn't seem truly evil, since she shows up to help the "good guys" a few times, but she's extremely detached and uncaring, especially when Sayaka dies and Kyouko (the otherJerkass Woobie) blows up at her for seeming so heartless. Of course, there's a (spoileriffic) reason for all this: Homura's a time traveller, and has watched all the other girls die extremely tragic deaths in numerous previous timelines. She keeps going back in an attempt to fix things, but always ends up making everything even worse than the last time. At this point, she's given up on everything except trying to save Madoka, despite knowing that it's probably impossible; she's become so detached because, otherwise, she'd lose hope and turn into a witch herself.
Alois Trancy. Alois is possibly the one of the most disgusting children ever seen in anime, and, most of the time, you just want to punch him for being such an ass. But don't tell me you didn't cry like a baby, or at least sniffle, at his backstory and untimely death.
And Angelina "Madame Red" Durless. Yes, she saw her first love choose her sister over her, and later both lost her Second Loveand her unborn child, which left her unable to have children and mentally/emotionally scarred to boot. No, this doesn't mean she's justified into becoming one half of the most monstruous assassin in Victorian England: Jack the Ripper. (The other half being a Shinigami named Grelle Sutcliffe)
At the end of season II, even Sebastian can count as this. That look on his face when he realized that he'd have to serve Ciel for all eternity and will never be able to eat his soul was absolutely disheartening for some fans.
Rip Van Winkle. Sure, she's a psychopathic vampire, but her over-the-top death at the hands of Alucard and her complete breakdown once he arrives elicits much sympathy.
How about Alucard for that matter? See volume 8 of the manga for more details.
Jean Croce of Gunslinger Girl qualifies. Throughout the course of the series, we see Jean as a revenge-obsessed jackass who isn't above torturing Padania agents, or even physically abusing his cyborg Rico. However, Jean's thirst for vengeance comes from the fact that his parents, his little sister Enrica, and his fiancee Sophia were killed by a roadside bomb planted by Padania to assassinate his prosecutor father.To make things worse, Jean's would-be brother-in-law hates him now, because he believes that Jean is doing nothing to get back at Padania, yet Jean can't confront him about it because of the secrecy of his work. And finally, to top it off, Jean's brother Jose has become an alcoholic following the incident, and ends up in a murder-suicide scenario with his cyborg Henrietta.
Nao Yuuki of the Mai-HiME anime. She's quite bitter towards others, uses her Child for selfish purposes, acts hostile toward Mai merely for being well-liked for caring for Takumi, and tends to cooperate only when she enjoys it rather than out of a sense of right and wrong. During the Hime Carnival, after her eye gets put out by accident, she swears revenge and tries to kidnap Takumi via Revenge by Proxy, indirectly causing his death, and tries kidnapping Natsuki twice. However, it's later revealed that her father is dead and her mother is comatose (causing her desire to seek vengeance on perverts), and after Nao's child is destroyed, killing her mother, and Shizuru is about to finish off Nao, Natsuki intervenes and says that if she had not met people like Shizuru, she might have turned out the same way, showing that, in spite of Nao's bitter and selfish attitude, she has suffered quite a bit and is ultimately human. By that point, Nao is a complete wreck, and ends up weeping hot bullet tears for her now dead mother.
Mariko Shinobu. She's selfish, clingy, creepy, acts like she owns Nanako and once tries to kill her, and at the start she's a bitch to Nanako's friend Tomoko. She's also one of Nanako's few friends in Seiran, protects her from bullies like Aya Misaki, and is very screwed up after her father first cheated on her mother, and later abandoned Mrs. Shinobu and young Mariko. She genuinely cares for Kaoru, and when Kaoru acknowledges it, Mariko becomes freaking adorable for a second.
Also, to the shock of many, Aya Misaki herself becomes one after she gets utterly broken by the last part of the TV series. To the point of being this close to commit suicide.
Sara of Tegami Bachi prevents all mail from coming to or leaving Honey Waters under the guise of being a Reverse operation, which results in the death of a man who tries to deliver on his own. But it turns out that she and Hunt had lived in a freak show, and Hunt had a dead creature's arms sewed onto him in a desperate bid to avoid being sold. When the people of Honey Waters happened upon them, Sara made up a story about Hunt being the Man Who Could Not Become Spirit in order to protect him from them, and all the other lies were necessary to maintain the first one. It helps that Sara gets a Heel Realization, leaves the money to the citizens, and leaves town with Hunt to start anew.
Lots of these show up in Fairy Tail. Looks like Hiro Mashima loves this trope.
JellalFernandez, Erza's childhood friend who, like her, was Made a Slave by a bunch of Zeref cultists, and ended up being locked up in a cell and tortured almost to death. Flash forward to the present time, and Jellal, after becoming Brainwashed and Crazy, getting a well-deserved revenge against the slavers and having completed the Tower of Heaven, had cooked up a plan to create the "World of Magic" where everyone would be free...which would require mountains of corpses, the sacrifice of Erza herself, and, generally, screwing things up royally for anyone who wasn't magically gifted. He had gone through so much hell in his short life that he thought no sacrifice was too great if it would mean nobody would have suffer like him. And just for grim irony, it turned out that his plan of reviving Zeref had no chance of succeeding from the very beginning, and that it wasn't Zeref who was speak to him. All in all, Base Breaker as he is, you can't deny that his life sucked.
He tones down the jerk and ups the woobie when he comes back free of brainwashing, and now with a horrible Guilt Complex over what he was made to do.
UrtearMilkovich, Big Bad Hades' right hand woman and the person responsible for Gerard's Start of Darkness, since it was her who spoke to Jellal's, pretending to be Zeref, was revealed to be one as well at the end of the Tenrou Island arc. Want the lowdown? When she was just an infant, she was separated from her mother Ur by a bunch of heartless scientists who wanted to use her for her immense magical potential. (Ur had asked for their help for her ill child. Those monsters took away the little girl and told her mother that Urtear had died from her fever and that her body was too horribly mangled for a mother to see.) Raised as little more than a sentient lab rat, Urtear was told that her mom had abandoned her and grew to resent her...but, most of all, she desired to go back in time to the moment of her abandonment and prevent it from coming to pass. In order to do so, she grew up into a brilliant and Machiavellian Chessmaster and Manipulative Bitch who would stop at nothing to awaken Zeref and uncover the World of Magic, confident that all her evil actions would be erased the moment she travelled back in time and averted the very event that sparked them. In the end, Urtear committed a lot of terrible things which were fueled by her desperate desire to meet with her mother and achieve some happiness for herself. When her plan failed, she fell into such shame and depression over what she had become that she tried to commit suicide to atone...and, ironically enough, she was saved by her Morality Pet, Meredy, a young girl Urtear had taken under her wing (after destroying her village...) and treated like a real daughter. Now, will someone please punch this woman in the face, and then give her a big hug?
The Oracion Seis except Brain were once slaves just like Jellal.
Suzu of Peacemaker Kurogane. Suzu becomes an insane Jerkass after he thinks that Tetsunosuke (his only friend) killed his master, Yoshida (whom he admired and was the only person who cared for him). He was taken in by a Depraved Homosexual old man and raped when he was alone and starving on the streets.
Alviss of M─R, after you watch his backstory and during the Ghost Chess Arc.
Sakuya Ookochi from Sensual Phrase. He's a Jerk Ass and a Bastard Boyfriend to his girlfriend Aine largely because of a scene where he attempted to rape her out of jealousy, and even when not being a Bastard Boyfriend, he's a huge jerk even to his own bandmates. Then, it's shown that he has an extremely Dark and Troubled Past (as in, he's an Heroic BastardChild Of Rape, his "father" left him when he learned that baby Sakuya wasn't his kid, he was bullied all the time because of his heritage, and his Lady Drunk mom drank herself to death when he was a child). While said past explains pretty well why he's such an asshole, it still doesn't justify his horrible treatment of other people around him, which had to be toned down in the anime quite a bit... and it still wasn't enough to make him anything but a Jerk Ass.
Karakuridouji Ultimo: Rune. By now, it's safe to say that he's done more things to garner Squick than sympathy from the fanbase. Especially to Yamato. But in a way, it's justified, as Ultimo did kill his past self. And then there's the fact that the current Yamato will never return the current Rune's feelings for him.
Murayama Musashi. While his whole world was destroyed, his rude quips to Yamato and tendency to rather recklessly do things himself places him in this territory.
Reika of Goshuushou Sama Ninomiya Kun is an arrogant Tsundere who frequently hits Shungo, but she also harbors feelings for him and frequently angsts over whether or not he likes her back. She has so much insecurity over her love for Shungo that she develops an alternate personality that comes out and attempts to rape Shungo in an attempt to convey her feelings to him.
Mirai Nikki: Tsubaki Kasugano, aka the 6th, and Yuno Gasai. And Yukiteru's always been The Woobie but he also becomes more unstable and more of a jerk as the story continues.
In Nausicań of the Valley of the Wind, Kushana, who is introduced in the film version as a seemingly steriotypical evil queen ("Nice valley. Think I'll keep it."), her status as an apparent Card-Carrying Villain is quickly subverted. This apparently was deliberate on the part of the writers: Miyazaki describes Nausicaa and Kushana as "two sides of the same coin", largely differing in that Kushana has "deep, physical wounds".
Rin from Kodomo No Jikan, especially in the earlier volumes. Yes, she has had a rough childhood and clearly needs to be helped, but the way Rin behaves - ways that could get a basically innocent man sent to prison, or seriously hurt someone - is just nasty. And she knows it.
Dr. Tenma from the 2003 version of Astro Boy. He's a control freak of a father to the point of abuse, yet watching the last few episodes one can't help but feel sorry for him.
Envy, from Fullmetal Alchemist: Brotherhood. He's cruel and utterly sadistic towards humanity- but only because he is actually jealous of their loving relationships and inner strength; neither of which the homunculi have.
Hayato Mikogami from Sekirei, the infamous Ashikabi of the South. He's extremely selfish and aggressively pursues any Sekirei that catches his eye, in order to add them to his growing collection. First introduced attempting to capture Kusano, he orders the injuring of the scientist that tried to protect her and is willing to order people killed if they get in his way. He comes across as ruthless, cruel, and utterly lacking in empathy towards his victims and his own Sekirei. Then he's revealed to be a Lonely Rich Kid, completely abandoned by his parents and unable to connect with his peers or make friends. He states that he felt empty inside, and desperately wished for "something amazing" to happen. The Sekirei he collects are the only friends he's ever had, and he expresses anger at the defeated ones for leaving him alone and wonders if he'll be reunited with them if he wins the Sekirei Plan. He's still very much a dangerous, ruthless enemy that has crossed many lines.....but it's difficult to not pity him just a little.
Shiki: The most prominent example is probably Masao. Although he's abominably uncaring and rude toward both the other teenagers and his family, he's also one of the least powerful and dangerous vampires, which results in his being the other vampires' punching bag on a fairly regular basis. Additionally, it often seems as though he has honestly no clue just why he annoys the other characters, to the point many fans have speculated that he has some sort of psychological disorder.
Kumiko Kotoura. A huge Jerkass to her own daughter by disowning her for unknowingly revealing her affair and considered to send her to the mental ward, however she lives in constant regret of the aforementioned disowning and failure to be a proper mother. There's also the fact that her husband refused to help with Haruka, put all the responsibility of 'fixing' her on her, and started not coming home. This combined with the Haruka problem drove Kumiko to drink and have the above mentioned affair. We all know how that turned out...
The said daughter Haruka is also one in the beginning of the story, for wearing a Jerkass Fašade so that she can be alone, partly as the consequence of the above. Manabe's seeing the "woobie" part of the trope was in fact the beginning of her recovery.