The doujinshi "From the New World with Love" has this spin on America. Starting out as normal and shocked by the loss of England or so he thinks, he decides "there is nothing left in Europe" for him, so after George Washington makes him promise to stay on his continent, he easily focuses on going westward. Then, inevitably, he reaches the Pacific and during World War One, he gets a letter from "Britannia", telling him there's no need to help out... which America interprets as a plea of help, understandably, given that it's written (or at least signed) in blood. Then he crosses the Atlantic... and things go downhill very quickly. So much, that by the time World War Two comes around, he's ready to let "Britannia"/England DIE, that is, if America gets the Hegemony from him. He takes the Hegemony all right... right from England's body. While saying that now that America took over England's duties as a superpower, England will have less work to do, and asks England to "come home". While he, or at least the monster inside his body, is tearing England apart, the real America seems to be in a dark limbo, desperately trying to call for England and find the way back. With much help from America, England wakes up from his coma in about the Eighties... but America is still Lonely at the Top and he knows that what happened to England, can/will happen to someone else in the future, because his body can't contain the monster forever.
Dawn Schafer from When Forever Wasn't Enough. She starts out as the closest thing to an Alpha Bitch the story has, attempts to further drive the already-existing wedge between the former BSC members, and is incredibly self-absorbed the point where she neglects Stacey's growing depression and accuses her of being the self-absorbed one. However, she is also shown to be struggling with self-esteem issues, and longs to go back to California where she feels she belongs. But the part where this trope really kicks in? After Stacey's suicide, Dawn is so devestated that she takes her grief out on the other girls and accuses them of not being there when Stacey needed her (pot, kettle; kettle, pot). While she continues to go through the stages of grief, she grows more rebellious and refuses to acknowledge that she wasn't there when Stacey needed her...until the girls start reading each suicide note Stacey addressed to them, and Dawn realizes that she wasn't there for Stacey when she needed her, which drives her to tears.
Caim from Mass Effect Human Revolution, a survivor of the Batarian slave raid on Mindoir who lost his parents there and discovers that the only way to hold the void at bay... is to kill, and kill, and keep killing. The Templars mould him into a xenophobic Master Swordsman.
Rika Nonaka from the Tamers Forever Series. Oh dear god, RIKA!! She is self-centered and mean, with an outrageous competitive streak. But it is physically impossible to read Silent Sorrow and not have your heart ache for her after seeing what the author puts her through.
Karkat, Vriska, and Eridan in the AU Brainbent. Karkat is a self-loathing mass of emotional turmoil and anger management issues. Eridan can be kind of creepy, but he seems to be a terribly lonely person, and there's something kind of endearingly pathetic about how darn awful his amateur fiction is. Vriska is a histrionic troublemaker (the "spread rumors that can ruin lives" kind, not the endearing-prankster kind), but her past was genuinely awful, and she has a lot of emotional problems under her badass facade.
Gamzee in Hivefled, especially the earlier chapters. He has an Ax-Crazy side he can barely control and does some pretty bad things to his friends (such as half-blinding Eridan), but he's also got a lot of issues and a truly terrible past that makes it hard to blame him for it a lot of the time. He is also at least trying to be better.
Hisao's friends saw him as this during his hospitalization in Weekend at Hisao's. They acknowledged that his life had changed for the worse and he was going through a difficult period, but they also saw him as hard to be around, which is why they stopped visiting after a few weeks. Thankfully, by the time he hears this, Hisao has gained perspective, as he did late in Shizune's route, and he renews ties with his friends.
Pretty much the entire cast of Eyes Without a Face. There are only a few characters who can be chalked up as pure Woobies, but the majority of them do things that make it REALLY hard to like them. Special mentions to Twilight Sparkle, Rose, Crest, and Baritone.
Another example from an MLP:FIM fanfic: Fluttercruel from the Pony POV Series. She is most certainly a Jerkass, but that's not entirely her fault as she was created by Discord and the only thing she came into existence knowing was how to be mean and cruel. Fluttershy manages to guide her from a complete Jerkass to a Jerk with a Heart of Gold (and in the Bad Future where this never happened, she apparently "grew up" into an outright monster). On top of that, due to how she came into being, she just sees herself as a "Fluttershy ripoff" and is physically incapable of having a life of her own, since, no matter what, she's just sharing Fluttershy's body and looks identical to her. She doesn't even consider herself alive. Yes, she's a jerk, but it's impossible not to feel sympathy for the poor girl.
Monkey D. Madelyn in Marie D Suesse And The Mystery New Pirate Age is a deconstruction of a self-insertMary Sue. By all accounts, she has done some terrible things, such as causing her brother Luffy to get captured and executed by the Marines, resulting in the deaths of several of his crew in the rescue attempt, and the deaths of all the others before long. However, it's later revealed that she did not actually intend for things to go this far, as she only wished to delay Luffy and his crew so that Law, the one she loved, could reach Raftel first; she is consumed with guilt as a result and ends up transporting herself into the real world, marrying and having a child, hoping to leave the mistakes of her past behind. Mar initially despises Madelyn for everything she's done, but after reading her diary and discovering that she's her mother, wonders if there are good qualities to her. Word Of God seems to confirm her sympathetic side, in response to a reviewer expressing sympathy for Madelyn.
That is indeed one of the main themes of the story neatly summarised. I wanted this to be a more realistic and accurate reflection of what causes a Mary Sue instead of a usual bash-fic, and no, I don't believe that most of them are created to be deliberately malicious in nature. I honestly think most of them mean well but just really don't know any better. As another reader noted, the road to hell is paved with good intentions.
Princess shows Julien with a bit of this. He's still his usual ditzy egotistical self, but he's going through a lot. He's Transsexual, and nobody around him knows enough about the condition to think of it as a legitimate problem.
In the Twilight fanfiction The (Not So) Short Second Life of Bree Tanner and its companion piece Ashes through an Hourglass, the offered back story of the Volturi's evil twin enforcers, Alec and Jane, helps rationalize their monstrous personalities in ways that elicit understanding and pity from the readers without undermining their sinister deeds. This more applies to Alec, though, since he has been featured far more than Jane and has demonstrated occasionally redeeming qualities through an amoral lens.
Allirea is at best amoral For Science!, and once sent a five-year-old to be tortured. She also has a personality-based power that allows her to hide and a Stalker with a Crush who regularly kidnaps her. And, since powers are personality-based, that means that what Allirea probably wants the most is some time by herself.
The characters Allirea and Addy have been conflated here: Allirea is a half-vampire who does have the witch power (and Stalker with a Crush) listed, along with associated personality. But the character who is amoral For Science! is ADDY, a full vampire with the witch power to "borrow" other witches' powers; her main goal has always been to find and train witches, so that she can try their powers and utilize them to their fullest extent, and it was she who sent the "five-year-old" to be tortured (to be fair, said five-year-old was a half vampire, and so was essentially a sixteen-year-old... which is only slightly better.)
Chelsea is a Mind Rapist, and screws up people's relationships regularly. She also has a desperate need to be loved, to the point that anyone she passes who doesn't love her disturbs her.
Angel, from the AU Roleplayverse Otherborn, is a half-demon who physically, mentally, and emotionally abuses his charge, Namine, who he claims to be in love with. In fact, he's come close to pushing her over the Despair Event Horizon more than once. Things went downhill when he was revealed to have killed his best friend in a jealous rage over the girl they both liked. And then... well, then the author started writing oneshots and revealed that Angel was, actually, so completely broken by this event that he literally went crazy. Namine was the only person who could put him back together again, but the damage done to his psyche was so immense that his demonic instincts began to take over, turning him into the Jerkass he is today. To the point where when Namine's abusive parents kidnap her back to their mansion, Angel goes into a catatonic state where the only thing he is capable of forming into a coherent thought is that he wants to die. The poor guy just seriously needs a hug.
Queen Anathema herself. The Big Bad, yeah, but what she wants is to just make a Utopia, and she has forgotten the costs of this due to grief at her lover's passing, she had to kill her own best friend when he turned against her and tried to shoot her numerous times, calling her a wretched villain for what she did. All she wants is love. Not to mention she is being manipulated by nearly everyone around her, even her most loyal man has betrayed her in the backstory, leading to a violent persona taking over and trying to rule through fear.
Shira. Raised as a girl to demean him by his psychotically misogynistic father, his mother was always out drinking and when she was home, she and his father always fought and ripped and tore at one another with their bare hands, leading to Shira getting a pretty nasty idea about what love really is. And when he came out as bisexual...it only got worse. Both his parents tried to drown him in a lake, while saying, "We love you too much to let you grow up a faggot." His discovery of his spell core in that very lake resulted in him accidentally killing both of them...and being psychotically devoted to killing, because otherwise he thinks they'd emerge from the lake as ghouls.
Rai-Dei Kurai. Yeah, he is basically Slenderman or something, annihilating almost everyone who knows about him. This is because he was not always an abomination. He was once a man, but was badly distorted by Stagnant Mana he tried to use to defend his mother and little brother from a murderous mob during the medieval times, as they were thought to be witches. He was haunted by the voices of those who died in the ensuing chaos of his ascent to One-Winged Angel, and wants to believe all the evil in the world can be traced back to him. He believes that the entire world, so inundated with evil due to him, needs to be purged, and is so crazy its no wonder he and Katherine Daille got along so well. He actually started to revert to a normality, but when Katherine was abused more fiercely, he felt that he could not fail a loved one again...