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Kagura from Inuyasha only serves the Big Bad Naraku because he holds her heart in his hands and can kill her at any time. She routinely helps out the heros, and when she allowed Kohaku to escape she was killed.
Androids 17 and 18. Before they became cyborgs, they were two teenagers who were kidnapped and used by Dr. Gero as experiments.
Vegeta was used by Freeza as a hostage and then had his father murdered and his entire race exterminated by Freeza, who continued to use him as a low-level enforcer afterwards. Goku eventually realizes that Vegeta was largely shaped by Freeza into becoming a remorseless killing machine.
Stella Louissier in Gundam Seed Destiny, due to being a brainwashed Super Soldier who was given Training from Hell since she was a young child and has a Control Word to keep her in line. The other members of Phantom Pain could also qualify, but Stella is the biggest example because of how childlike and broken she is, and her love for Shinn Asuka.
As you go down the line from the One Year War, you'll find Zekes and Feddies both that get caught up in a Cycle of Revenge as the previous wars left them scarred and without purpose but vengeance. The most recent example of this is Loni Garvey from Gundam Unicorn, the daughter of a former Zeon soldier who brought the remnants together, she lost her parents in a Feddie hunt for remnants and it has consumed her such that all she wants is vengeance for that.
Fist of the North Star: Shin, originally Kenshirou's best friend, is tricked into becoming a Big Bad due to his weak heart by Jagi, who convinces him to kill Kenshirou to get his lover, Yuria, whom Shin has long had a great desire for. He tries to please Yuria with every luxury he gains with his bloody hands, but to no avail. When Yuria commits suicide - or at least, she seems dead - to prevent him from doing it any further, Shin is left heartbroken, and finally joins her in the afterworld after his defeat in the hands of his former friend, Kenshirou.
Souther also qualifies as a Tragic Villain - a particularly cruel, tyrannical type. Overrun by the grief of killing his own beloved adoptive father and master, who instructed him to do it to complete his training, he goes insane and orders children to build a pyramid for his master without mercy until Kenshirou kills him, making him reveal his human side at his death.
Nike, TheAx-CrazyDragon to Air Gear'sBig Bad, fits this. While he's a mostly unrepentant jerkass who kicks the dog often and balances over the Moral Event Horizon, he does generate some sympathy. He's been used as a weapon for most of his life by the brother he looks up to and one of the characters harmed most by Nike even states that his brother kept him isolated from everything that could have dulled his edge. As a result, his life gradually lost all meaning outside of killing to achieve victory in battle. When he finally realizes how close everything that could have given him a normal life was, he seems to lament the fact that the other Gravity Children could have given his life meaning instead of just his bastard of a brother. However, he feels that even if he's finally realized this, he's come too far and that there is no way he would be able to live a normal life. The way the scene plays out, it makes it feel like he's a slave to his own need for victory.
In Code Geass, either Lelouch or Suzaku or both could apply for this: They've both done morally dubious things in the hope for a better world, they've both demonstrated a great deal of regret and guilt over what they've done, and yet they both feel that they have no other choice but to continue down their current path.
Continue, nothing. It is their tragedy that makes them start walking on that path in the first place - it is only after accepting that they have no choice but to walk the morally dubious path that they truly do things that would be regarded as villainy.
Mao may count as well, since the reason why he's a villain stems from the Geass he received at the age of six. Unlike most examples, though, he doesn't seem to be aware that he's evil.
For that matter, if one is to consider C.C. (the one who gave Mao and Lelouch their Geass) a villain, then she also qualifies, as she was an innocent girl who was tricked into inheriting the power of Geass and immortality.
Some of the Un Dead in Shiki hate what they have become, but the pressure from other vampires combined with their uncontrollable bloodlust and desire to live mean that they can't stop themselves. The best example would be Tohru.
Also he subverts this trope. He's genuinely surprised when Renamon saves his life and offers him a second chance, and actually turns her offer down since he thinks death is all he deserves. After some persuasion on her part, he relents and becomes a Reformed, but Rejectedatoner, although he still doesn't think he can nor deserves to be redeemed.
Lucy from Elfen Lied is one of the prime examples of this trope: A broken little girl who became a murderous monster after she snapped at the world's relentless cruelty and her own budding insanity.
The Akuma from D.Gray-Man could count, especially the ones given backstories, like Mimi, Crea/Claire from the first few episodes, and the witch from the witch arc.
Naruto: Character Development revealed that Gaara's psychosis was a direct result of the actions of his own father's attempts to either turn him into a living weapon or kill him. Insanity and Shukaku's whispers were his last refuge from the bleak emptiness of his childhood. Thankfully, he does a Heel-Face Turn and life starts getting better for him. As the series has progressed a majority of the villians has turned out to be this with notable exeptions being Zabuza and Orochimaru.
Even then you can make a case for those two. Zabuza proved to truly care about Haku, and his death truly did break his heart and drove him to Suicide by Cop. Orochimaru lost his parents at a young age and desired immortality to see their reincarnations. Originally he wanted it for himself and the entire village, but eventually his increasing thirst for power and descent into insanity made him lose sight of his original goal and made him into what he is today.
In all actuality, the only real exception to this trope in Naruto is Hidan. He killed his neighbors and ditched his village because the village itself became a tourist resort and abandoned the whole ninja village thing. The lack of violence went against his religion.
Conversely, one of the most tragic is the Big Bad, Tobi, aka Obito. Tobirama's revelation of how the Uchiha Clan's deep sense love is also the source of their "curse" and subsequent insanity changes the perspective of Obito's supposedly disproportionate reaction to Rin's death. The mental anguish truly was worse for him, and to see the girl he loved killed by his best friend was something his mind couldn't handle. He clings to the Assimilation Plot of Madara not because he honestly wants to make a better world, but because it can give him back the person he loved the most: Rin.
This is shown while his soul was being devoured by the bijuu, which was represented by his genin team photo being torn apart and being reconstructed when he regained his sanity. Even after all he has done and said, it seems his friend, his crush and and his sensei are his reason to exist.
Even Madara Uchiha has shades of this. While no doubt one of, if not THE most villainous character in the franchise, it was a result of a life filled with tragedy. He was born in the era of Warring Clans, one of the most violent periods of time in shinobi history. By the time he was ten, he had already lost four brothers, leaving only Izuna, and the constant loss and desperation caused a dream of peace, a dream he shared with Hashirama Senju, the future First Hokage and Madara's best friend. However, despite that dream, what Madara cherished most was Izuna, his only remaining brother — enough to willingly turn his back on his best friend and his dream for his little brother's sake. Hashirama believes that all of Madara's actions are a result of him lashing out in his grief over his brother's death.
Rosine from Berserk was an abused child who sacrificed her parents to the Godhand.
In fact, all of the demonic Apostles, the main villains of the series, were once humans who made a Deal with the Devil during a moment of ultimate despair.
The King of Night in Is This a Zombie?. He grew to hate his immortality and just wanted to die. However, Yuu saw him as a friend still and didn't want to kill him, so the King went out and caused everything that happened to get Yuu to hate him and thus kill him.
Adolf Kaufman from Adolf. He was forced to go to Adolf Hitler Schule and became a true Nazi who killed without compassion. He crossed the Moral Event Horizon, which made him lose his friends and family. He realized at the end of the war that what he did was useless, but it was really too late for him to have any chance of rehabilitation.
In Sonic X, Dark Oak, also known as Luke/Lucas, counts as one, as his tragic past happened during a war that took place on his former home planet of Seedrius-Flora/Greengate. Refusing to leave with the other Seedrians and abandon his home planet after having fought so long, he began using its Planet Egg to make the male Seedrians' transformations last longer to Hertia/Earthia's shock and dismay, forcing the females to destroy the males and leave them behind. But a few males survived and they became the Metarex. The motivation of Dark Oak and the Metarex is to erase all life of flesh and blood from the entire galaxy so that plants can rule, and therefore bring their own peace and tranquility to the galaxy, and they require the Planet Eggs and the seven Chaos Emeralds to do so. In the end, Dark Oak finally realizes the errors of his ways when Sonic and co. defeat him with help from Cosmo's Heroic Sacrifice - he realizes that Hertia/Earthia was right about his lust for power destroying his own people and him bringing nothing but pain and suffering to everyone. Hertia/Earthia appears before Dark Oak and gives him a second chance, and he happily reunites with her and they both depart for the afterlife.
Gluttony from Fullmetal Alchemist. Despite embodying his Father's gluttony, Gluttony is a near invincible overweight manchild who would rather eat and spend time with Lust like a child to his mother than actively hurting anyone beyond eating them. No doubt tears were shed when he himself was eaten by the Pride, calling out to Lust (who died earlier in the series) to help him.
Scar in the Brotherhood anime is an (from Anti-Villain to Anti-Hero) example. When asked what is his name, says that Ishvalan names are from God and implies that he doesn't deserve to be called by his real name anymore. Also when Winry hates him for killing her parents after they helped him due to his confusion at the time and tries to and contemplates whether or not to kill him, he understands and seems at peace with the idea of her getting her revenge on him and dying as a result.
Wrath in Fullmetal Alchemist was a sweet, normal kid when introduced. He eventually warps into an antagonist but he mainly just wants a mother. It isn't until The Movie that he realizes that he had Izumi the entire time, though by than she's succumbed to her ilness.
Annie Leonhart, Reiner Braun, and Bertolt Hoover from Attack on Titan, in a series of major reveals that create more questions than answers. All three are Tyke BombChild Soldiers sent to destroy the Walls and infiltrate the military as The Mole. While their crimes may well have put them over the Moral Event Horizon, a fact they even acknowledge, there's no denying that they are painfully human. The narrative paints them in a sympathetic light, focusing heavily on their conflict over their mission as well as their guilt and trauma over the things they have had to do. While their exact motives remain mysterious,they claim their actions are must be done and that they can't stop — making them either Necessarily Evil or Trapped In Villainy.
Fate/Zero shows that Kotomine Kirei started off as this. Kotomine Kirei lived his life always trying to do what others and his society thought was good, because he found he could only find happiness in violence, destruction and tragedy and despised himself for this. However, Kirei questioned if others truly were as good as they said they were but followed what he was told regardless, becoming an Executor (assassin) for the Church despite understanding the hypocrisy. When Kirei met Gilgamesh, Gilgamesh slowly convinced Kirei to stop hating his genius and to use it for what he truly enjoyed.
In B.Ichi, the Clowns must respect a specific condition in exchange for their power, or they will lose "something precious within them" (like "friendship"). Some conditions are rather harmless (like "eating only dried food"). Emine's condition is… not. He must commit "one evil deed a day", which prevented him from getting along with normal humans, as much as he wanted to. He ends up so desperate that several years later, he is determined to kill Showtaro and destroy the world. How did all this end? Who knows…
Helbram from Nanatsu No Taizai is presented as this. He was once a kind fairy who was fascinated by humans until he saw his beloved friends tortured and slaughtered, leaving him as a hateful shell of himself. His hatred for humans had swelled for years up to a point wherein he can no longer bring himself to stop killing humans despite his own desire to do so.
Prior to the aforementioned animated series, Mr. Freeze was just a generic Silver Age kooky tech-based villain: B:TAS came up with the idea of Mr. Freeze as a man simply wanting to restore his wife and every incarnation since (except for the one in The Batman) has adopted this aspect.
Although in the New 52Nora isn't his wife, she's a frozen woman from the '40s with a heart disease. Freeze is just crazy.
Depending on the Writer, fellow Batman foe Killer Croc can also be seen as one of these. Yes, he's a homicidal cannibal, but he is often portrayed as having little to no control over those urges. His increasingly bestial appearance and the gradual loss of his own humanity (again, Depending on the Writer) makes it impossible for him to have any sort of life other than that of a villain. In his appearance in the Titans series, he mentions that all he wants now is to be left alone.
Wonder Man, long-time Avenger, has been straying into this. After being revived, he's become increasingly disillusioned with the perpetual cycle of superhero-supervillain violence. After repeatedly asking the Avengers not to re-assemble, he puts together a team of similar malcontents (including a new Goliath, angry over his uncle's death during Civil War) who attack Avengers Mansion and Stark Tower, demanding that the Avengers be disbanded.
Ballade is also this. He realized that being the robot Wily's most proud of meant others will fight for the spot, and while he showed respect to his enemies he got no respect from comrades.
In The Tale of Discord, well, DISCORD OF ALL PEOPLE is this. Let me count the ways. His father was disgusted by his appearance, barely anyone treated him like a normal citizen, his crush (Celestia) didn't return his feelings (though they didn't exactly hate each other back then), and then these events happen: his best friend, Luna (the mare he now knows he loves) feels that Discord betrayed her and she leaves him in tears. This is only the first part of his Start of Darkness. He later learns that his doting and ailing mother died giving birth to his sister (who would begin the line of the Sparkle family. Well, whaddya know?). This sends Discord on his path of chaos (but not before taking care of his dad.). If that doesn't make it any sadder, it is revealed that the spirit of Nightmare Moon was possessing him and judging by his behavior nowadays, he is permanently scarred by his past. By the end, you just want to give him a hug!
Films — Animated
Stinky Pete from Toy Story 2. All his actions were evil because, for years, no one bought him.
Lots-o-Huggin' Bear from Toy Story 3 as well. He became heartless and completely vile because he was abandoned (not intentionally) and was replaced. Unlike Stinky Pete, Lotso never sought redemption.
Lord Shen from Kung Fu Panda 2. His plan to conquer all of China is essentially an attempt to get over his Parental Abandonment issues and find happiness. He himself even admits that it probably won't be enough.
Tai Lung from the first film also counts. He Used to Be a Sweet Kid before being rejected the scroll of the dragon warrior, which led to him turning on his father figure.
Rise of the Guardians has Pitch Black, the Boogyman, who is unhappy because unlike other fairytale characters, children fear him instead of loving him.
Hans from Frozen, according to Word of God, had never been loved, and the way his brothers treated him was downright cruel, resulting in him growing up to be a sociopath.
Films — Live-Action
Koba from Dawn of the Planet of the Apes. While Caesar grew up with kind caretakers and recognized the good in humanity, Koba spent much of his life being tortured and experimented on by his captors at Gen Sys. He's fiercely loyal to Caesar after he liberates the apes, but grows more and more paranoid that the surviving humans will wage war. By the end of the film, he's become even worse than the humans he grew to hate and fear.
Dr. Sebastian Caine in Hollow Man. After he achieves invisibility, he becomes a homicidal lunatic and rapist, but his mind was being warped by the experimental treatment. The longer he spent invisible, the harder it would become to be able to go back after that.
Star Wars: Darth Vader/Anakin Skywalker. Sure, he's pretty evil (although nowhere near as evil as Emperor Palpatine/Darth Sidious), but the prequel trilogy made him go from just Luke's evil father to Luke's tragic evil father. The expanded universe makes this more apparent. He's aware of what he's done and hates himself for it and feels beyond redeeming. Which is why he continues down his path.
Michael Corleone in The Godfather Saga. He starts as an independent minded War Hero, but he is gradually dragged into mob life to protect his father and his family. He fought his perceived enemies with cold ruthlessness for years while he struggles to achieve legitimacy, and by the time he gets there, he admits that it's too late and that he is too tired and past redemption, and passes the torch to a new Don.
Pirates of the Caribbean: Davy Jones falls into this category, since it was his love for Calypso and her betrayal that caused him to do the things he did, including telling the pirates how to lock her in a human body.
Godzilla. The original 1954 film Gojira showed that he was as much a victim of the atomic bomb as everyone else.
Loki from Thor. He was motivated by a combination of sibling rivalry with Thor, the desire to impress his father, personal ambition, and a messed up sense of duty towards Asgard. There is also probably a fair dose of self-loathing, seeing as he found out that he was a Frost Giant and not an Asgardian.
He is also portrayed as this in The Trials of Loki comic miniseries.
Hans Beckert of M doesn't want to murder children, but just feels compelled to do so. His speech at the end (wherein he calls out the Mob hunting him down on their ruthlessness) reveals just how tortured and screwed up he really feels.
The Villain Protagonist of The Headless Eyes, a burglar who loses his eye in the very first scene and slowly loses his mind as well, winds up becoming this by the end of the film, to the point where even after everything he's done in the course of the film, the audience still feels sorry for him as he freezes to death in a meat freezer without ever having found a real solution to his eye problem.
The Sandman in Spider-Man 3 never meant to kill Peter's uncle or cause trouble for anyone. All he wanted was to get enough money to save his little girl.
Mama/Edith in Mama. In the film, due to her mentality, her baby was taken from her, and she went through extreme measures to get her child back. She then commits suicide by jumping off a cliff and her baby ends up on the branch while she lands into the water. It's implied that she doesn't even know where her lost child is. She also kills and threatens people who she thinks wants to harm Victoria and Lily. All she ever wanted was to be a good mother.
While usually many of James Bond villains tend to avoid this trope being pure evil and lack of redeeming qualities, there are few exepctions.
Alec Trevelyan/Janus from GoldenEye. He wants revenge on the British government after it betrayed his parents, Lienz Cossacks, and sent them back to the USSR where Joseph Stalin had them all executed. Though Trevelyan and his family manage to escape the execution, Trevelyan's father was ashamed to have liven his life as a Lienz Cossack, and he purposely killed Trevelyan's mother and himself out of survivor's guilt.
Elektra King from The World Is Not Enough. She was kidnapped by the terrorist Renard and held for ransom, which her father refused to pay on the advice M. Embittered by what she saw as her father's betrayal, she participated in Renard's scheme to milk money from her father.
Raoul Silva from Skyfall. He was turned over to the Chinese in exchange for four other agents. They tortured him, but he refused to give up his secrets. Upon learing it was M that gave him up, he tried to commit suicide, but the cyanide didn't work, but left him disfigured.
2014 Disney movie Maleficent tells the story of Sleeping Beauty from the perspective of the villain of the original story, Maleficent, who seeks vengeance after her fairy wings are taken.
Oz: The Great and Powerful reveals that the Wicked Witch of the West came to be because she was too naïve to realize that her sister was playing her and agreed to bite a magic apple that turned her into a merciless Axe Crazy villain. Oz is partly to blame for that, as he flirted with Theodora like he does with any girl he meets, making it easy for Evanora to claim that Oz courted her too while showing pictures of Oz with Glinda. Even Evanora is disturbed as to how Axe Crazyher sister has become.
Pamela, the mother of the infamous Jason Voorhees. A prequel comic shows that she gave birth to Jason as a teenager, and suffered much spousal abuse from husband Elias. She eventually murdered him and struggled to raise her disabled son on her own, which eventually led to his fatal drowning at Camp Crystal Lake. Losing her only family pushed her over the edge, and she went on a killing spree to ensure no child ever has to go through what Jason did.
John Kramer AKA Jigsaw started out as a decent man, a loving husband and a soon to be father. His wife was mugged by one of her patients at the drug clinic she ran. She lost her child in a miscarriage during the mugging. The two went through a messy divorce and John later contacted cancer. After being denied health insurance, John grew disgusted seeing people unappreciative of the gift of life he was being denied. He devoted himself to kidnapping people and placing them in life threatening situations to try and get them to appreciate life.
His apprentice, Amanda Young, also counts. When she was a little girl, her father would lock her in a dark closet and keep her there for hours. In her adult life, she was framed for a drug crime she did not commit, and became an actual drug addict in prison. She was later kidnapped by Jigsaw and placed in a situation where she had to kill to save her own life. She came to see Jigsaw as a mentor and father figure, and became his apprentice due to Stockholm Syndrome. Even after her Face-Heel Turn she still had it pretty rough, being thrown into a pit of needles and almost being killed by Xavier Chavez. Finally, she was blackmailed by her rival apprentice Mark Hoffman.
Harry Osborn/ Green Goblin, played by Dane DeHaan. He was neglected and belittled by his obsessed, sickly father Norman and on top of that, inherits his own fatal disease. He begs Peter to help him get Spidey's blood in order to synthesize a cure. Peter suggests things could turn worse and tells him this as Spidey too, but Harry is desperate for anything that will save him, even if it kills him. When he finally does get the blood, since it's designed with Richard Parker's blood and thus why it only worked on Peter and failed with everyone else. It turns him into Green Goblin and he blames Peter/Spidey even more, especially when finding out about his dual identities. While what he wants throughout the movie makes him identifiable and understandable, it doesn't make causing Gwen's death easily forgivable.
Max Dillon/Electro. Abandoned and mistreated by nearly everyone (even his own mother who fails to remember his own birthday and interprets his humming hint as annoying singing in a deleted scene) and with just Spidey giving him encouragement, he got into an accident involved electric course because of said mistreatment, and everyone are either ignoring him or treating him as a true menace (unlike Spidey who this time around are more welcomed by the public), so he's had enough and decided to lash out to humanity for all their mistreatment to him.
Lucian Carr from Kill Your Darlings has the distinct ability to manipulate both the characters in the film and the audience into pitying him. Furthered by the revelation that he met David Kammerer, who he kills at the climax of the movie, when he was just 14 and had been stalked by him ever since.
In Inception, Mal really has no choice about being a psychotic, murderous, obsessed Femme Fatale. She just wants to be with Cobb forever, but the villainous Mal in Cobb's dreams isn't even his real wife, but a shade of the dead woman he can't bear to forget. The dead Mal herself was brainwashed by Cobb, but inadvertently became so obsessed with the notion of her world not being real that she killed herself and framed Cobb for it. All out of love.
American Me: Montoya Santana, a Mexican gang leader, is portrayed mostly as a product of his environment. He was the product of rape himself, became acquainted with youth gangs in his neighborhood, was sent to Juvie where he was raped, murdered his attacker only to be convicted of murder, and has had to remain the top dog ever since simply to survive.
Unbreakable: Elijah Price is desperately looking for a purpose in life. He thinks that being a supervillain is better than being nothing, so he commits several acts of terrorism to find his antithesis, a real life superhero. He expresses deep remorse for what he has done to complete his life's work, but thinks he finally knows who he is.
The titular vampire of Blacula. Once an African prince, the evil Dracula turned him into a vampire, sealed him in a coffin to starve for two hundred years, and killed his wife. Blacula hates being a vampire and is shown to feel remorse for his actions. Blacula only feeds on people because of his hunger, and clearly regrets it. At the end of the film, he ends up being Driven to Suicide.
Kitty Galore from Cats & Dogs 2. A Fallen Hero, she was once an agent of a secret organization that fought for the rights of both cats and dogs. On one of her assignments, she was investigating a chemical plant. A dog scared her and made her fall into a vat of chemicals. She lost all her fur, was ridiculed by her fellow agents, and upon returning home, her owners threw her out on Christmas of all times.
Clyde Shelton of Law Abiding Citizen. His wife and daughter were killed in a robbery, and the more guilty robber got a slap on the wrist while the less guilty one got sentenced to death. Infuriated with the justice system, Clyde set out to destroy it, causing the deaths of hundreds of innocents in the process. Even after everything he has done, it is hard not to feel sorry for him.
Cujo isn't really a villain in the popular sense of the word, but he's just as much a victim as anyone else is, and if the Cambers had taken the possibility of their dog catching rabies seriously, the disaster could have been avoided. Parts of the books are told from his perspective; there it's shown that he suffers horribly from rabies, and only attacks people because he believes that they are responsible for his pain.
Claude Frollo from Victor Hugo's The Hunchback of Notre Dame suffers from his obsessive love for Esmeralda, which causes him to go tragically insane. What makes his suffering sympathetic is the fact that he was a deeply compassionate and caring man before he laid eyes on the gypsy.
Murtagh from the Inheritance Cycle. During Eldest, he is enslaved by Lord Galbatorix and forced to fight on his side. Brisingr makes it appear that he's gone completely evil at first, but Eragon speculates that he's getting back at the world for giving him a crappy life. Near the end of the book, he's fighting the Dragon Rider Oromis and he desperately screams at him, "YOU COULD HAVE HELPED US!".
His dragon, Thorn, counts as well, as he wonders why he was brought into the world just so he could be tortured and destroy things.
Galbatorix's dragon, Shruikan, is one of these as well. While Galbatorix remains a villain, several characters point out that Shruikan never chose to serve him; his real rider was killed when he was a hatchling and he was forced to bond with Galbatorix, driving him insane. When he finally appears in Inheritance, he is a nightmarishly huge and powerful dragon that appears to be an Omnicidal Maniac; Elva tells Eragon that nothing is left of him but pain and hate, and the best they can do is end his suffering.
The entire town of Dark Falls in the first book. They were all once a normal, thriving community, but an accident at the nearby chemical factory caused gallons of toxic gas to engulf the citizens, transforming them into vampiric mutants. Now, they have to feed on new visitors every year to survive. At the end, after the protagonists have destroyed most of the residents, the real estate agent responsible for ensuring new victims is the only survivor. The ending implies he'll continue his gruesome business, all alone.
The creature from ''Frankenstein is driven to evil when everyone (including his eponymous creator) rejects him because of his monstrous appearance. In the end he tries to take his revenge on humanity before committing suicide.
(Only in the book; the movie adaptation replaced all this with "Science Is Bad".)
The Hunger Games: Just about any of the other career tributes. Yes, they are all ruthless and one even taunts Katniss about Rue's death but they are all teenagers being forced to fight to death in a Crap Sack World
Agents of S.H.I.E.L.D.: Ward is revealed to be a Hydra sleeper agent. However, his backstory is tragic on so many levels that (as of the Season 1 finale), much of the fandom is hoping for a redemption arc.
Barely an Averted Trope by Zack Allan. He joins Nightwatch because he thinks it's an extra 50 credits per week for the work he's already doing, but over time finds that he's joined an organization with darker goals. He's in over his head, and struggling with the ethics of his previous decision—but he can't leave Nightwatch without causing himself more trouble. It's not until Captain Sheridan and the rest of the senior crew offer him a way out that he's finally able to escape his dilemma—thankfully, before he's forced to perform any actual evil.
The entire run is essentially a long tale of this, as Walter White starts out forced into his life of crime as his only way to care for his family, but eventually starts choosing evil and caring only about himself.
His "accomplice" Jesse may not have started out out innocent, but without Walt he would, at worst, have stayed a clueless bottom-of-the-ladder meth cook. "Thanks" to Walt, he's helped build an incredibly lucrative drug empire - at the cost of his sense of self-worth and almost everything he cares about. The worst part is that at least two of the big things he blames himself for are squarely Walt's fault, he just doesn't know it.
The Master, especially during the two-parter "The End of Time".
The Minotaur in "The God Complex". He doesn't want to kill, but does so in order to survive and feels at peace when it finally dies.
Game of Thrones: Theon Greyjoy. He has done some terrible things, but it was all because he was torn between two families - the family that raised him and treated him well but held him from his blood family as a hostage, and his blood family who gave him up in the first place and now treats him like dirt. Once he made his decision, there was no going back, and he could only sink further and further down as he tried to find a place to fit in. And then, after he is tortured brutally and finally escapes, he admits that he chose wrong and that he betrayed his true family, the Starks. And then he's brought back to be tortured again.
Gamel, one of the Greeed, is by far the most sympathetic of the Greeed, being a childish simpleton who doesn't care about doing evil things, and only wants to make Mezool happy. He's still The Brute, and has absolutely zero regard for anyone's life but Mezool's, but his puppy-like devotion makes his eventual death (both of them) feel very sad.
Mezool counts as well: her driving desire is to experience parental love. She is quite satisfied with treating Gamel as her child until she receives a Hannibal Lecture that pushes her over the edge, all the while lamenting the impossibility of her dream (Greeed cannot reproduce) and the unquenchable nature of her desire.
League Of Gentlemen: Practically everyone (well, maybe except Mr. Chinnery who is a Tragic Hero and Hiliary Briss and Papa Lazarou who are just downright evil...) is one of these.
LOST: Michael Dawson, who murdered Ana Lucia and Libby and delivered Jack, Kate, Sawyer, and Hurley into the hands of the Others because it was the only way to free his 10-year-old son and get him off the Island.
Regina blamed Snow White for the death of the man she loved, instead of her mother who actually killed him because of a mix of fear and need for acceptance. Her need to destroy Snow causes Regina to kill her own father and cast a curse that exiled her and countless others into the real word, but she still feels empty because no one loves her. She adopts a son but her need to control him alienates him. Her backstory shows she was tailor-made to be the villain and even when she tries to get better she's afraid she won't get her happy ending because "villains don't get happy endings".
Rumpelstiltskin keeps losing everyone he loves because of his need for power.
Owen spent his whole life trying to get back to Storybrooke and rescue his father, only to find he's already dead. Owen also turned out to be Peter Pan's Unwitting Pawn
Prison Break: FBI Agent Alexander Mahone, the main villain in the second season, is only trying to murder the protagonists because the Nebulous Evil Organisation is blackmailing him (they know he murdered a Serial Killer), on top of threatening to kill his wife and child.
Revolution: General Sebastian Monroe. It's not obvious at first, but as the first season goes on, it turns out that he is this. He was once a good man and a soldier for the USA, but a number of events occurred. First, he lost his entire family in a car accident and he would have killed himself had Miles Matheson not intervened. So he attaches himself to Miles to the point of borderline erotic fixation ("Nobody's Fault But Mine"). The blackout also happens, leaving a lot of people, including Miles and him without a job ("Pilot"). Miles and Monroe form the Monroe Republic, with Monroe as the general in charge ("No Quarter"). Their relationship fell apart when in response to a Rebel bombing the restaurant they were in and injuring Miles, Monroe had the Rebel and his entire family executed to make an example out of them. Miles tried to assassinate Monroe in response but he couldn't do it. A number of times, Monroe points out that he never really cared about controlling anything, and that he thought he was just doing what Miles would have wanted ("The Dark Tower"). A number of times, it is also shown that Monroe doesn't enjoy being a villain, but he apparently feels that there's no going back for him ("Home").
Supernatural: The Archangel Michael in season 5 frees Lucifer to bring about the Apocalypse, which will destroy at least half of the planet. Yet he is ultimately trying to make the best of a bad situation with holding everything together after God's abandonment and looking after humanity. Bringing about the Apocalypse is supposed to please God, destroy the source of evil in Lucifer and Hell, and bring about paradise both for humanity and angel. Ultimately, he is trying to fulfill his duty and please his Father even if that means killing the brother he loves.
Makuta Krika from BIONICLE. He didn't agree with Teridax's Evil Plan, nor with him overthrowing the Brotherhood of Makuta's former leader and turning the organization evil, but had he rebelled, Teridax's supporters would have killed him. After realizing what the plan entailed, he became resigned to his fate: if it succeeds, they would become the rulers of a world he wouldn't want anymore, and if it failed, they would face the wrath of a Physical God. Too late did he find out that Teridax wanted to rule alone. Upon trying to warn his brethren, they believed him to be a traitor, and killed him.
Three Days Grace's song "Animal I Have Become" could be interpreted as being about one of these.
Other songs that seem to portray this trope seem to be especially prevalent in the metal and punk genres, such as:
Sweeney Todd is a classic example. Having been exiled by a corrupt judge who then took his wife and fostered his daughter, he returns for revenge and to save his family. When his vengeance is denied, he teams up with Ms. Lovett, who makes the worst meat pies in London. Her meat pies become much better when Sweeney Todd starts murdering every man who comes to his barber shop and giving the bodies to her to use. Yet despite being a mass murderer who helps dupe people into eating human flesh, Sweeney is still usually portrayed as a Woobie and Villain Protagonist in the musical. His original incarnation in penny dreadfuls was a lot less sympathetic.
Elphaba of WICKED, in a perspective flip of the original plot of The Wonderful Wizard of Oz. The Wicked Witch of the West started out as a solitary young woman frequently derided as hideous just because she has green skin. Everything good she tries to do backfires spectacularly—in no particular order, she loses the only teacher who cared about her, is forced to leave her best and only friend G(a)linda (The Good Witch of the South), loses her little sister Nessarose (The Wicked Witch of the East), and her lover Fiyero who she unknowingly turned into the Scarecrow in an attempt to save his life. By the end of the play, she's suffered so many failures that she completely loses it and her death is devastating to the audience and Glinda. And Glinda is the only one who DOESN'T knowElphaba faked her death.
The Phantom of the Opera, who comes across as pitiful even as he does a multitude of horrible things, all of which he seems to have been driven to do because of his horribly disfigurement.
Nathan did commit a series of crimes in Thrill Me, but he also had a peer group of one, and that one was a rather poor influence.
The Suikoden series might be king of this trope. In literally every one of the primary five games, one or more of the primary antagonists are this.
Suikoden I: Emperor Barbosa's apparent lapse into psychotic madness is actually a desperate gambit on his part to redeem his new wife, the insane Wendy, who reminds him of his first wife, who'd died tragically. He ultimately pisses away his legacy, his friends, his kingdom, and his life trying to help the woman he loved… who didn't want his help.
Most of Barbosa's underlings count as this (with the notable exceptions of Yuber and Neclord). All his generals, including the protagonist's father, are fighting for Barbosa out of loyalty and honor, not because they don't think he's crazy.
Suikoden II: All the major villains except Luca Blight and Yuber (again). Jowy, the main antagonist and the protagonist's lifelong friend, is trying to do the exact same thing the protagonist is doing (trying to stop the war and unify the land for the sake of everyone), but he's doing it from the opposite side. Leon Silverburg, his genius strategist, is trying to end things as quickly as possible for the same reason, but the protagonist's side's competence ends up dragging everything out.
All of the Blight family's underlings, like the generals of the previous game, serve the empire because they loved Luca's father, not because they don't think Luca is a total shit (and he is).
Suikoden III: The main villain is one of the heroes of the previous two games, trying to stave off universal entropy. His second in command loves him too much to understand the cost of what he's trying to do. Yuber is also there, and remains as non-tragically evil as ever.
Suikoden IV: The Man Behind the Man is arguably one of these, but the main general you spend most of the game building towards a confrontation with, Troy, just loves his country and wants to protect it.
Suikoden V: The first major villain, Queen Arshtat, is the hero's mother and is being driven insane by the rune she bears, which she only agreed to bear to protect her country. Her sister, Sialeeds, later performs an apparent Face-Heel Turn in order to go full Big Damn Villains from the inside, but it costs her big and turns her into one of these. The main villain, Gizel, is a racist jerk, but he's a racist jerk who legitimately thinks he's doing the right thing for Falena because he listens to his much jerkier father.
Gizel is given a much more tragic bent in the manga, where it's implied the true reason for his villainy is because the Succession Crisis of the royal family killed his mother and destroyed his Perfectly Arranged Marriage with the only person he ever loved.
The Grand Theft Auto series has a few villains/criminals with tragic backstories:
Trevor Phillips from Grand Theft Auto V has a very Dark and Troubled Past. He has a history of rage issues and violent impulses that ruined his attempts to fit into society. Besides that, he suffered numerous social problems: he grew up with a physically abusive father and an emotionally abusive mother.
Final Fantasy IV has Golbez, really Theodore Harvey, Cecil's brother, who may cross the Moral Event Horizon several times in the game, except that he was under the control of Zemus and takes full responsibility for his actions once freed from Zemus's control.
In the DS remake, it's much worse. The implication is that Golbez wasn't brainwashed, and that it was the darkness in his own heart that led to him being controlled. The remake makes a much bigger deal out of his Reformed, but Rejected status after the spell is broken.
In Batman: Arkham City, Mr. Freeze doesn't have it much better in the game than he does in the comics. His wife is still frozen, and he's blackmailed by the Joker for the TITAN cure, leading to him getting captured by Strange and thrown to the Penguin, who proceeded to torture him, giving him woobie status until the Batman came around. Eventually he did reunite with her, but only if you're willing to endure that side quest.
Mass Effect has most of the decoy Big Bad throughout both games, via varying forms of Mind Control and Mind Rape. Matriarch Benezia, the Collector General (the whole Collector race), Shiala, even Saren gets a few sympathetic moments, despite being established as a Knight Templar long before Sovereign got his tentacles into him. The Collector General especially gets quite a few fan-tears shed over its death.
Harbinger of all people is one; the Extended Cut reveals that the Catalyst destroyed its creators and used their genetic material to create him...meaning he's the last of that first race, and is stuck serving the guy who destroyed them forever.
The Catalyst itself, after the Leviathan DLC and Extended Cut; the Reapers' overmind is little more than a broken tool, unable to fix itself or even realise that it's broken, built by ancient aliens with a massive god complex to ensure their organic slaves weren't killed off by synthetics they built, but whose arrogance prevented them from realising that it could view them as part of the problem and turn on them. It can't fix itself; that's what the Crucible is for, but since that Crucible also offers the possibility of destroying it and bringing an end to its great work, it also strives to eradicate the Crucible designs whenever possible.
Clone Shepard - brought into being solely as a reserve set of internal organs, awakened by a particularly vicious racist even by Cerberus standards to serve as a figurehead and a tool to replace the real Shepard, and then confronted with an endless chain of reminders that they just weren't up to the level of the original Shepard and never would be. Finally, the one person the clone actually seems to care for abandons them in a scene heavily inspired by The Mummy Returns, leaving them with nothing. Even if you try to save them, the clone will simply let go of the Normandy's ramp, hundreds of feet above the Citadel streets.
Red Alert 3: Yuriko Omega, born Yuriko Matsui, was kidnapped by Mad Scientist Shinji Shimada and transformed into a Tetsuo-like psionic monster with no feeling of empathy toward anyone else, particularly because she was bullied by her schoolmates due to her natural psionic ability that caused her tragic fate. She even went through hell to find and save her sister, who turned out to just want to be at the top of the world, just like other people, including the Allies. After doing what has to be done, Yuriko still remained a lonely, unloved girl, vilified continuously by the news media of the major global powers (all Allies, the Soviet Union, and Japan).
All four main antagonists in the Fatal Frame series. All of them were nice people when they were alive, it's only when they died and were corrupted by their respective gates to Hell that they started killing everyone.
Sniper Wolf from the first Metal Gear Solid is defined by her tragedy—she's a Kurd whose childhood consisted of being a fugitive and refugee who lost her friends and family to an Iraqi gas attack, who was taken under the wing of Big Boss, who truly regrets her part in the Shadow Moses incident in her last moments. However, even Psycho Mantis and Liquid Snake are tragic in their own ways, the former fueled by a childhood of his father's hatred and neglect, where the latter is driven by a massive inferiority complex for which he blames his (blameless) father.
Fortune of Metal Gear Solid 2: Sons of Liberty was an ordinary woman until a conspiracy to steal Metal Gear RAY took place. She lost her father during the Tanker Incident, her mother to suicide following the event, her husband to death in jail due to a federal fraud case, and her unborn child to miscarriage due to the stress. It's no surprise that a woman who lost everything would want revenge, and at the same become a Death Seeker as well.
The End of Metal Gear Solid 3: Snake Eater is a grandfatherly figure who spends most of his time barely conscious, only really 'coming to life' to snipe. He bears no ill will whatsoever towards Naked Snake, and challenges him solely to find a Worthy Opponent before he dies. He won't even kill Naked Snake, as he only ever shoots tranquilizer rounds. The most tragic figure in the game, however, is The Boss herself. She was a true patriot.
In inFAMOUS, Kessler, reveals to be Cole from the future who has turned Empire City into Hell just so that he could turn his past self into the savior of the world from The Beast.
Thanks to the events of Birth by Sleep, Xemnas from Kingdom Hearts, of all people, was given shades of this. His original persona, Xehanort, happens to be the end result of Terra being body snatched by Master Xehanort and then both of them being subsequently locked out of this new being's heart, leaving the man with only about a year's worth of memories. Then he loses himself to darkness yet again, with his leftover body and soul (Xemnas) having nearly no memories whatsoever to draw upon and suffering from Wistful Amnesia about the friends he can't entirely remember (Aqua and Ventus), much to his frustration and chagrin. Xemnas might share a lot of traits in common with Master Xehanort, but the small flickers of Terra's personality within him and the life of the mind-wiped Xehanort himself make him seem almost pitiable. When Sora asks Xemnas if he can remember all of the feelings in a heart besides anger, rage, and hate and Xemnas replies with an almost sorrowful "Unfortunately... I don't," he's not lying. That line becomes even worse when you remember that it was Terra's own hatred of Xehanort that essentially led to him becoming Xehanort.
All the Nobodies and members of Organization XIII qualify, as they didn't ask for their non-existence and lack of hearts, but are forced to live with them nonetheless.
In Iji, the final boss of the game, General Tor, is the leader of the fleet invading earth to eradicate the last of the Tasen. However, he only does this because he's a Slave to PR. There were many generals including Tor himself that wanted to end the war without committing genocide, but the rest of the Komato insisted on doing so because they hated the Tasen and wanted them dead. He gives in to finally attacking the remaining Tasen, and is about to completely destroy the Earth to make sure no Tasen are left alive, at least until the protagonist arrives to prevent Tor from doing so. Once he's defeated, he sees the error of his ways, calls off the attack, and saves whatever life is left on Earth in the process. Unfortunately, the guilt of killing so many people in the past weighs heavily on him, and he kills himself so he doesn't have to live with it anymore.
The Transcendent One from Planescape: Torment. All he wants is to live and preferably to never again meet the main hero, whose very presence reminds him of the times when he was a part of the hero's soul rather than an individual sentient being, and he cannot stand it. Unfortunately, the hero's quest to regain his memory and mortality means that confrontation is imminent, and to prevent it he's prepared to murder everyone who could possibly direct the hero to him.
Super Paper Mario: Count Bleck. His motives were entirely the result of grief over the supposed death of his girlfriend, Timpani.
World of Warcraft is full of villains with tragic back stories. One of the most infamous villains is Arthas, a paladin prince who was desperate enough to save his people against the undead scourge that he committed many terrible acts to stop the onslaught, up to taking the cursed blade Frostmorne and losing his soul.
Illidan wanted only for the woman he loved to return the affection and practice his beloved magic. Every action he took saw him rebuffed by those closest to him, but he still clung to the belief that he could do some good. After being exiled for using demonic magic to fight the Burning Legion, he tried and failed to destroy the Lich King. By the time of Burning Crusade, his constant failures and rejections have driven him mad.
Another villain who was reintroduced in the Cataclysm is the dragon aspect Neltharion the Earthwarder, one of the five dragons created by the titans to protect Azeroth from the Old Gods' corruption. Unfortunately, while he was in a 1000 year rest, the Old Gods managed to whisper to him, driving Neltharion mad and causing him to devastate the other dragonflights and gain a new name for himself: Deathwing the Destroyer.
Shiro Tagachi from Guild Wars would fall under this catagory, but only after you learn his complete backstory. He was a skilled soldier who defended a local village from bandits and robbers. He was well liked and was quite the hometown hero, until the Emperor took notice and hired him as a royal bodyguard. The dark god Abbadon took advantage of this and began planting the seeds of doubt and paranoia into Shiro through the use of demonic agents disguised as fortune tellers and members of the royal court. It got Shiro so flustered that he decided the only way he could safeguard his own life was to kill the emperor and acquire ultimate power so that nobody could ever betray him. What he didn't realize was that by now, the general public viewed him as a monster. By the time you meet him in Factions, he's so far gone and filled with Abbadon's corruption that he seems incapable of listening to reason.
More than a few in Dark Souls, mostly qualifying more as Tragic Monsters, though the best example is Gwyn, Lord of Cinder, former Big Good of the Age of Flame and (possibly) the greatest impediment to mankind's Golden Age.
The Gods, the reason they turned against Kratos was because Kratos released the evil within Pandora's Box, which affected them greatly.
Whoever the traitor in Dawn of War II is. All have sympathetic motives.
Tarkus believes he is being Necessarily Evil, and can use the power of Chaos to save his brothers.
Thaddeus sold his soul in exchange for safe passage through the Warp for the Litany of Fury, so the Blood Ravens' recruiting worlds could be saved from the Tyranids.
Jonah has been possessed, and is desperately trying and failing to regain control of his own actions.
Cyrus has seen how utterly corrupt the upper echelons of the Blood Ravens have become, and how little the foot-sloggers mean to them, and has bartered for the power necessary to change leaders.
Avitus cracked when he found out that his justification for the destruction he caused was a lie, and that so much blood had been shed for no reason. In his mind, the best case scenario is Suicide by Cop, the worst case is that he'll continue doing what he apparently has done for years, but without the veneer of lies.
Malia Gedde was the great-great-etc. granddaughter of Tetelo, a voodoo priestess whose tribe's traditions included such things as cabrit sans cor. Malia herself had no ill will toward Gabriel and even seemed to be in love with him, but Tetelo's influence forced her to attack him and abduct his friend.
Friedrich von Glower was the son of a baron who raped a young Gypsy girl and became cursed to lycanthropy as a result, and the curse was passed down to Friedrich himself as well, transforming him into "The Black Wolf." Despite living for centuries as a werewolf and committing countless slaughters, von Glower seemed to believe that the werewolf curse could be controlled, and he seriously wanted to control it.
The Legend of Zelda: A Link Between Worlds features Hilda. Her plan to have Yuga steal Hyrule's Triforce stems from her desire to replace Lorule's Triforce after it was destroyed to keep anyone from using it, only to cause Lorule to rapidly fall apart. It's not until Ravio convinces her that doing this would simply leave Hyrule to the same fate as Lorule that Hilda realizes the folly of her scheme.
R.O.B., a character that was previously nothing more than an NES peripheral, spends most of Super Smash Bros. Brawl's story mode as one of these. His homeland was invaded and turned into a bomb-making facility, and he was forced to deploy the bombs and pull the world into Subspace. He switches sides after one of his bosses forces all of his comrades to pull a mass Taking You with Me and detonate every bomb in the facility, but this sadly results in him becoming the last of his kind.
Kirei Kotomine, the Big Bad of Fate/stay night. He was born with a mental defect that made it so that the only thing he could find pleasure in was the suffering of other people. However, he still had a conscience, and every time he enjoyed someone suffering, he recognized that it was wrong. Disgusted with himself, he tried out a number of different vocations in the hopes that he would be able to enjoy one without bringing harm to others— he even married an Ill Girl, whom bore him a child. But when she killed herself to try and prove that he could feel emotions, he realized that he would have been more satisfied if he had killed her himself. He gave up at that point, setting the plot of the game in motion.
Also Archer in the Unlimited Blade Works route, who fought so hard to be a hero and save people, only to break under the realization that he couldn't actually accomplish anything, leading to his desire to kill his past self before he can pursue that path.
Every villain, with the notable exception of Junko Enoshima from Dangan Ronpa and Super Dangan Ronpa 2. They all kill because of the horrifying situation they've been put into.
Jeff The Killer used to be a normal kid, before the Terrible Trio of Randy, Troy, and keith tried to mug him and his brother. Jeff beat the bullies up, but they lied to the police and said Jeff attacked them first. Jeff's brother took the blame to protect him, and was sent to juvie. Already dealing with the guilt and the loss of his brother, Jeff was attacked by the bullies at a party, where they beat him close to death and set him on fire. The trauma from these events caused him to snap and become a Serial Killer.
Red vs. Blue gives us the Meta/ Agent Maine. He starts out as a relatively ruthless solider, but he is still loyal and protective of his teammates. After losing his voice defending one of his teammates, he is given the A.I. Sigma, who slowly corrupts Maine until his former personality is completely destroyed, leaving only the Meta. By the time season 6 comes, he has been reduced to little more than an beast. Even without Sigma controlling him, he is still compelled to fulfill Sigma's ambitions simply because that is all he knows.
Beware the Batman: Most of the villains on the show fall into this, especially if you exclude those affiliated with the League.
Magpie's probably the most heart-wrenching example, as she started off as a basically good person with kleptomania, but the treatment they gave her (which she volunteered for in hopes of being cured) ends up shattering her mind, and eventually erases her good persona entirely. Even after that, the Magpie persona is largely sympathetic, as beyond her compulsion to steal she mostly just wants to be loved; it's her complete lack of impulse control and her own emotions that makes her a villain. Even Batman feels sorry for her, and of course because it's that kind of show his attempt to help her only makes things worse.
Metamorpho's another one, as none of what happens to him is his fault and if any of the major players in his life would just treat him with a little kindness everything would be fine. They don't.
Humpty Dumpty is yet another one, and is equally heartbreaking. He tried to do the right thing by testifying against his Bad Boss Tobias Whale, but was horribly injured and driven insane by Tobias' vengeance. Humpty is left basically a super (tactically) intelligent child, who mostly just wants to play games. Unfortunately, his games involve (somewhat justifiably) getting even with the people who either attacked him or failed to protect him, so he ends up drawing the attention of Batman, who naturally tries to help me. It doesn'twork.
And then there's Lunkhead. He used to be a basic (albeit strong) mook, but a fight with Batman left him comatose and damaged his brain. Nowadays he's basically a gigantic child who *wants* to be good, but is just a little too stupid and immature to control himself. At one point he's coerced into breaking out of jail (which he initially doesn't want to because he knows he's been bad and belongs there) with the promise of candy. And, once more with feeling, because it's that kind of show he doesn't even get the candy. Instead, he gets betrayed by his only friend and pushed off a ledge.
Adding to the list, there's Jason Burr, who starts off as a straight up good guy, and still wants to be one, but suffers from residual effects of Cipher's mind control that force him to betray his friends and try to kill his love interest.
In the most recent episode, we find out that Katana's father, a well-intentioned guy for the most part, was blackmailed into betraying his best friend Alfred, making him one of these. And, again, because it's this show he dies for it.
The Ice King assumes this role when it is revealed in a Wham Episode that he used to be a normal human with a fiancé, whom he called his "princess". His Artifact of Doom ice crown made him go insane and made his fiancé leave him when he just tried it on for a laugh, and turned him into a hermit that constantly kidnapped princesses, subconsciously trying to get Betty back.
A later episode actually reveals Betty didn't abandon him, as she was running in fear from him in his insanity, The Ice King from the future had temporarly turned back to normal and opened a portal through time to say one last goodbye. Though Betty basically says "Screw that" and jumps through the portal into the present day Ooo determined to find a way to permanently cure him
Marceline is more of a jerk than a villain in the earlier seasons, but her backstory is quite tragic, yet not being as evil as other examples.
Lemongrab. He is a creation with mental problems, it is impossible for him to have a social relationship for that condition (which it has led to suicidal thoughts), is uncontrollably impulsive, his mother locked him in his castle for a long time, bullied him and has long been in his own solitude. The Lemonjon's death probably contributed much to his Ax-Crazy behavior (note that he has in his mind thoughts like "rage" suffer "), as well as a revelation in the second videogame.
Magic Man is probably one as well. He seems to live deeply depressed by the death of his girlfriend, and that's the reason why torture other creatures.
Mr. Burns is characterized for being one of the most iconic and greedy villains in the entire history of Western Animation. However, in his childhood he was a Cheerful Child, but his grandfather, a cruel and insensitive man, was the reason why he is the man we know today. He lured him away from his loving parents and forcibly adopted Burns. There's also the loss of his teddy bear, Bobo, but that may or may not have actually contributed to it.
Plankton. It is known that as a child, he was bullied and his only friend was Mr. Krabs. Now he is evil and despises society, not only because of this, but also for a dispute with Mr. Krabs for poisoning the old man Jenkins.
Roger Smith from American Dad!. It is implied that he is so evil because his species releases a bile that kills them if they don't "let their bitchiness out". Made worse when it is revealed the reason he is trapped on Earth is that the others of his species wanted to get rid of him.
Worst part is He beat the heroes and started to travel back in time. Only reason he didn't win? He was only able to go back 20 minutes in time, just barely enough to save the Sadida from extinction.
Avatar: The Last Airbender: Prince Zuko. The snarling, angry, ruthless teenager turns out to be a "Well Done, Son!" Guy who just wants to return home and be loved by his father. Who mutilated him and then exiled him from the kingdom on a lifelong Snipe Hunt over his speaking out against a plan to use a squad of raw recruits as cannon fodder to bait a trap for an enemy regiment.
His sister Azula too, in a different and arguably MORE tragic sense. While she seems to blatantly be a Manipulative Bastard and The Sociopath (our first sighting of her is of her smiling with joy as her brother gets his face burnt), it eventually turns out that her viciousness and cruelty were encouraged by her father, but her Daddy's Little Villain training alienated her from her mother and she has no idea how to interact with others without fear and manipulation.
Zuko and Azula's great grandfather Sozin as well. Despite leading a genocide and killing his best friend, Sozin reflects at the end of his life whether all of it was worth it. He somberly concludes that it wasn't and dies a sad and regretful man seeing his life as a waste, despite what the Fire Nation history books would write.
From The Legend of Korra, both Tarrlok and Amon/Noatak. The sons of the very evil Yakone who trained them to bloodbend seeing them as nothing more than possible tools of vengeance against the Avatar and Republic City. Yakone's abuse of both him and his brother caused Noatak to run away and conclude that bending was the ultimate evil, becoming a self-loathing Knight Templar and taking on the identity of Amon. Tarrlok eventually becomes a ruthless politician in Republic City and only at the end does he realize that he's become the very tool of vengeance that his father wanted him to be, just as Amon also did, having torn Republic City apart socially and politically. With this realization he decides to end both his life and Amon's in a Murder-Suicide.
Amon: Noatak. I'd almost forgotten the sound of my own name.
Demona from Gargoyles. She seems to be aware, on some level, of her evil, but can't stop doing it or even consciously admit it to herself because that would require her to admit that much of the suffering she's experienced over her millenium-long life was her own fault. So, instead, she's the ultimate Woobie, Destroyer of Worlds, lashing out at the world around her in the hope that, if she kills enough humans (and anyone else who gets in her way), it'll be enough to make the hurting stop. She's definitely a villain who needs to go down, but you can't help but feel sorry for her, all the same
Several established Batman villains are portrayed this way in Batman: The Animated Series, as people whose lives have been consumed with a desire for revenge on the people who caused their problems. Mr. Freeze is probably the best example.
Freeze: Think of it, Batman: To never again walk on a summer's day with the hot wind in your face and a warm hand to hold. Oh, yes. I'd kill for that.
Even sadder, is that Nora is eventually revived but Mr. Freeze refuses to let her see what he had become, so she (possibly an amnesiac) runs off to get married with her doctor offscreen which in turn destroyed what little humanity Mr. Freeze had left
Baby Doll is a former actress with a growing disease who prevents her body from developing, so that she will always look like an 8 year old kid. After a brief success in a sitcom that starred her as the troublemaking kid in a typical American family, society shuns her and she loses everything. She finally resolves to kidnap the cast of her old sitcom in a desperate attempt to live her fantasy of a "normal" life.
One-shot villain Lock-Up may not be the best person on Earth (he's cruel to inmates under his charge as the warden of Arkham Asylum) but considering he's right that the legal system in Gotham encourages Batman's rogues gallery to keep coming back, putting everyday people at risk, he goes over the deep end into villainy himself because he's fired for being too tough. While cruelty isn't good by any standards, the fact that he was working with people like the Joker and Scarecrow means he was effectively canned for not being nice enough to serial killers and professional terrorists.
Then there is Calendar Girl who is getting revenge at the modeling world after they fired her for being too old (she is in her late twenties at least) and making her ugly. When the mask comes off she is beautiful but is absolutely horrified seeing her own face. Best put by Batman.
Batgirl: She's beautiful.
Batman: She can't see that anymore. All she can see is the flaws.
Lord Garmadon from Lego's Ninjago. Bitten by the Great Devourer and infected with his evil, he cannot fight that side of him. He struggles to be a good father to his son Lloyd and lets him make his own choices and follow his own destiny, even if it means that the two are destined to battle in the future.
It is implied that the cruel treatment Eric Cartman receives from his schoolmates for being fat and his Butt Monkey status in previous seasons (abducted by aliens and being teased by Scott Tenorman) made him the sadistic Ax-Crazy psycho we know today in "Scott Tenorman Must Die". That, and he hasn't known who his father was for the longest time, causing him a not insignificant amount of grief. In the lack of a readily-available father figure, he turns to sometimes-dubious substitutes, most notably Chef.
Professor Chaos, Butters's villanous Secret Identity in the season 6. After the main boys snub him, he adopts the alter-ego "Professor Chaos", and plots to drown the world... with a garden hose.
Scott Tenorman, the villain of the 200/201 episodes. While he was not such a nice guy before the events in "Scott Tenorman Must Die", still counts.
Dr. Drakken of Kim Possible became a villain after his college friends laughed at him, one of which was the father of his Arch-Enemy.
World from Fosters Home For Imaginary Friends. He destroyed his own world in rage when the gang tried to take Frankie back home, but he has a tragic backstory and the fact that all he really wanted was a friend who was willing to stay with him.
Vicky, implied. It is possible that she has a Freudian Excuse for her actions and had Dark and Troubled Past which made her the way she is now? The episode "Snow Bound" suggests that she had rough childhood. Later episodes, however, Flanderized her to be so evil, even her parents are afraid of her.
Crocker wants to destroy all fairies due to losing his own fairies as a child, and became the Ax-Crazy, Sadist Teacher we know today.
Eddy from Ed, Edd n Eddy was the Villain Protagonist of the show, but it was not until The Movie, where it is revealed he was a victim of Domestic Abuse by his older brother. At the time, he tried to find a way to impress him. After that revelation, is confirmed that he's definitely the most tragic character in the series.
Cat from CatDog is Temporarily a Villain and a Jerkass Woobie in some episodes. But he gets beaten up on a regular basis by the greasers dogs, and always gets hurt because of Dog running around and bumping to what ever is in his path, and he suffers the repercussions of whatever Dog does.
Averted in The Powerpuff Girls with Mojo Jojo, who claimed that he was once Professor Utonium's faithful lab assistant who was ignored following the girls' creation and his transformation into an Evil Genius, thus leading him to become a villain. In reality, he was a destructive chimp who broke everything he touched and Professor Utonium finally threw him out after the girls were born.
Dreadwing and Predaking. The former is an honourable warrior who went berserk upon learning of the desecration of his brother's body and the later is a revived Predacon who, thanks to Megatron's manipulations, ended up all alone in the universe.
Megatron himself used to be an idealist freedom fighter who could see the injustice and corruption of the society he lived in. But his lack of understanding of things like kindness and tolerance made him walk down a dark path that eventually led to the death of his own planet.
Vlad Masters in Danny Phantom qualifies as this. When he was at college with his former best friend and crush, said friend accidentally mixed up the material needed to make a ghost portal work, which led to him becoming a ghost hybrid and him hating the culprit because of it. Years later, he discovers his creator's son who also suffers from his condition. He offers him the chance to help control his powers, but also to rule the world with him and abandon his father. He then pursues both the boy and his mother and hopes to destroy the one who started it all. However, he fails and tries making clones of the son to have as his own, but his hopes are dashed, which leads to his Villainous Breakdown.
Nightmare Moon from My Little Pony: Friendship Is Magic. Once, she was Princess Luna, one of the two royal sisters who saved Equestria from Discord, freed the Crystal Empire from King Sombra and ruled over Equestria with her sister, Princess Celestia. She felt that no one appreciated her night because they slept through it, which led to her becoming resentful toward her sister and attempting to bring about eternal night. She is returned to the side of good early on from the main protagonists' intervention.