"A character who, although acting for primarily 'evil' or selfish goals, is either not in full control of their actions or emotions and the reader or viewer can sympathize for due to them not being evil by choice; but rather by them being a victim of circumstance. These villains can face a crisis of conscience in which they submit to doing evil. These villains often have confused morals believing that they are doing moral when in fact they are doing evil."
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.
Hokuto No Ken: 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.
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 take note that 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.
Rosine from Berserk was an abused child who sacrificed her parents to the Godhand. There's also Griffith, who crossed the Despair Event Horizon. 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 Kore wa Zombie desu ka?. 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 several times, 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.
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.
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.
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 Trails 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.
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 totally 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.
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.
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.
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 arguably 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.
Barely averted 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.
Michael Dawson from LOST, 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.
FBI Agent Alexander Mahone, the main villain in the second season of Prison Break, 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.
Gamel, one of the Greeed in Kamen Rider OOO, 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.
The Master from Doctor Who, 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.
The entire run of Breaking Bad is essentially a long tale of this, as Walt 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.
Theon Greyjoy on Game Of Thrones. He has done some terrible things, but it was all because he was totally 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.
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.
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.
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.
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 Uion, 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.
In Infamous, Kessler, reveals to be Cole from the future who have 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.
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 enjoyment 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.
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.
Super Paper Mario: Count Bleck. His motives were entirely the result of grief over the supposed death of his girlfriend, Timpani.
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.
For some, Plankton from Sponge Bob Square Pants could be seen like this. 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.
Squidward is an interesting case. While he's not an straight villain, it is believed that much of his evil and cruel acts are due to being an unsuccessful guy with bad luck, and having to live and work with SpongeBob, which makes life miserable especially in later seasons.
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.
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.
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.
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.
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.
The Ice King from Adventure Time 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.
Lemongrab embodies many evil qualities: he's overly-controlling, harsh, often mean and cruel, unsympathetic to anyone... But his excuse is that he's a) a failed experiment with mental problems, and b) only about one year old.
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.
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.
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.
Meg Griffin from Family Guy is an odd example. In several episodes where he shows his dangerous and psychopathic behavior, she's always Temporarily A Villain, but it is obvious that all this is due to the cruel treatment that everyone has towards her, especially Peter, Lois and Connie.
Eric Cartman from South Park probably could count as this. It is implied that the cruel treatment of 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 sociopath we know today.