Fruits Basket: whether or not one can excuse his or her actions, Akito counts. Despite beating the living daylights out of several Zodiac members for the majority of their childhood(s) and emotionally abusing everyone, Tohru can't help but feel sorry for him or her. One, she learned just how badly Akito herself was emotionally abused, and how her upbringing influenced her outlook on life. The psychological abuse heaped onto her by her mother and Evil Matriarch extraordinaire, Ren, led to a pathological fear of abandonment, driving her to do anything to make sure no one will leave her. Being told that no one loves you, everyone will abandon you, and no one even respects you, and having your boyfriend sleep with Ren to spite you for sleeping with another man (which you partly did to get back at said boyfriend, and partly to stop said man from abandoning you) will do that to you.
Dr. Hell from Mazinger Z. Everyone (including his parents. In particular his mother 'repeatedly' complained she never wanted having him, and hit him for any reason) abused him and mistreated him during his childhood and teenhood years until his mind finally snapped out, and he decided one day he would purge the world off idiots, and everybody would have to bow down to him. He was still dreaming of doing just that several decades later when he finally found the means to do so as exploring the ruins of an ancient, lost civilization.
Madam Red from Black Butlerbecomes "Jack the Ripper" to get back at prostitutes for giving up what she could never have, with the help of Grell Sutcliff.
Vincent from the Cowboy Bebopmovie, having gone self-destructively homicidal from psychosis and the inability to separate his hallucinations from reality after becoming an unwilling participant in a Super Soldier program that caused him to permanently hallucinate. His leitmotif "is it real?" just hammers it home.
Lucy from Elfen Lied. Several characters think that it's her natural instinct to eradicate humanity, but given her past, her experiences alone would be enough to make her what she is. She truly believes that she doing all those atrocities out of instinct, so if we look at the nurture aspect, we come to the conclusion that she Mind Raped herself (with a little help from nearly everyone around herand an inner voice / alternate personality that wants to eradicate all life) into believing that she was, in her own words, "born to wipe out mankind". Heartbreaking can't even begin to describe it.
Mantid from Spider Riders — he loses the love of his life in war; it's implied that he lost many friends the same way; now this is just a theory, but it may be that he lost his spider partner as well, which makes sense because we never get to see it. With all that, it's no wonder the guy went off the deep end.
Shinji Ikari turns into this during End Of Evangelion. After spending the entire series watching/hearing most of the friends he made die in the most horrifying ways, then having to accept that his father never loved him and was never going to, then having to decide to continue piloting the EVA for the world's sake, and then having to kill the only person who showed genuine love for him for his father's sake, maybe it was a mistake to let him decide what will happen to mankind.
At the end of Magical Girl Lyrical Nanoha A's, Hayate Yagami became one, though it required a massive Break the Cutie moment created by other parties to push her past the "the-world-has-hurt-me-so-much-it-deserves-to-die" breaking point, and when she regained her senses, she chastised her Artifact of Doom for thinking that that's what she really wanted and put a stop to things.
The Book of Darkness is another example. Her life cycle has three phases: charging up in dormancy, gaining full awareness and control for a few minutes, and then dishing out an Earth-Shattering Kaboom, which returns her to stage one. Prior to her current appearance, she has been forced to serve a cruel master who abused her children. Bonus points for the fact that there is nothing that can be done to stop the cycle.
Another one in Magical Record Lyrical Nanoha Force: the Huckebein family seems become this. Sure, they have to try to find a way so they could control their Eclipse disease. But their unsympathetic actions, like slaughtering entire villages and communities, massacring the innocent people who had nothing to do with their affair is not a justifications for their reason to survive.
Trigun features Legato Bluesummers, The Dragon to Millions Knives. He's got a sympathetic backstory as a nameless sex slave and, like Knives, has let his own pain drive him into becoming an Omnicidal Maniac. Problem is, he's an utter, sadistic psycho with a murder habit, who likes to torture the lead, reducing any sympathy factor for him both in-universe and out.
Hiroko "Hiro-chan" Kaizuka from Narutaru is an intelligent, modest young girl who is broken by abuse from both unbelievably sadistic bulliesand overly demanding, repressive parents. Eventually, she, along with her Shadow Dragon, Oni, attempts to make everything she doesn't like disappear...by way of going on a horrific, murderous rampage.
A similar thing happens to the main character, Shiina, but with someone else doing the destroying, right at the end of the manga.
A lot of characters from Deadman Wonderland probably qualify, but the crown here definitely goes to Shiro/Wretched Egg. Despite the horrific things she does on screen, by the time her backstory is fully revealed (and goodGodisittragic), even Ganta agrees that his worst enemy isn't nearly as much of a monster as he first thought.
Elaine and Diana, the two unbelievably powerful psychic sisters, in Genocyber, who both go through some truly nightmarish crap before transforming into the eponymous Anthropomorphic Personification of destruction, Genocyber. Then they proceed to wipe out Hong Kong, then every single city in the world, then the only post-apocalyptic city that remains. Or maybe not...
Gaara in Naruto started out as this. He's lucky Naruto is a Warrior Therapist. For that matter, any jinchuriki (such as Naruto and Gaara themselves) is prone to be so.
The Nine-Tailed Demon Fox's escape plan is to turn Naruto into one of these.
In Part II, Sasuke Uchiha becomes this after hearing the truth about the Uchiha massacre.
No, actually the biggest example is Tobi. He watched his only love die and the hands of his best friend, and at that point, he resolved to destroy the world and remake it in his image, or maybe Madara's image, it's hard to tell the difference anymore. In the span of a few months, he went from saying that those who betray their comrades are worse than trash to holding his sensei's newborn son hostage, killing his sensei and his sensei's wife, nearly annihilating his entire village and when his sensei's dying act thwarted his efforts, he plotted the extermination of his own clan. Nagato unleashed his woobie-induced rage on his enemies; Tobi unleashed it on his friends!
It doesn't help that Tobi is genetically prone to being a Woobie, Destroyer of Worlds.
Yuuhi from The Lucifer and Biscuit Hammer, with a Freudian Excuse to match: his father, a detective, was killed by his colleague. After the funeral, his mom simply left, and his grandfather beat into him the idea "Make no enemies - they'll stab you in the front; make no friends - they'll stab you in the back." Sami's reasoning is that she wants to own the world by destroying it so that it doesn't go on without her when she dies.
Valgaav from The Slayers TRY. A tormented half-demon dragon who believes that all cosmic forces in his world are caught in an endless, senseless war that only causes suffering, and wants to erase everything from existence to end this.
Black WarGreymon from Digimon Adventure 02 wanted to destroy the Digital World because he thought that, that was the only way for him to understand his purpose in his artificial life and soothe his pain.
Yukio Oikawa from the same series. Growing up as a lonely boy in a unforgiving world, the only friend he ever had was Cody Kida's father. During their youth, they became the very first humans ever to discover the Digital World, and they together promised that they would one day travel to it. Fate decided to be a mean bitch one day and killed off Hida during his line of duty as a police officer before it could happen, leaving Oikawa with no one else in the world but his promise. Depressed and lonely, he became a easy target for Myotismon's ghost to possess, who promised him that he would help him to get to the Digital World and fullfill his promise to Hida...at the expense of everything and everyone else.
Darcia from Wolf's Rain, who, after the loss of his lover, Hamona, turns insane and decides to ruin the paradise the protagonists are trying to create. In a sense, he doesn't want to destroy the current world, as the Earth is dying anyway, but prevent the next.
Rau Le Creuset from Mobile Suit Gundam SEED. He's a dying man at 28 years old, born with telomeres of the thirty-something Al Da Flaga, his genetic "father". He's in constant pain that can only be subdued by drug dosages that double twice over the course of the series. His dealings with people, hatred of his flawed body and the people who ensured that he was born that way, his emotional pain over his Parental Abandonment, and being a clone and thus seeing himself with no "identity" of his own eventually became a bitterness towards humanity in general. He descends into full Nietzsche Wannabe territory, convinced that humans only inflict pain and suffering on others, not least of all himself. Aware that his own existence cannot be considered human and is more or less the personification of mankind's sins, he took it upon himself to be the Judge, Jury, and Executioner of humanity, and in a very literal bid to make the pain stop, he tried to Kill All Humans, and nearly succeeded.
By the time he sentenced all of humanity to annihilation, he was more or less reveling in the fact that his view was "vindicated" by the actions of Murata Azrael, who had just tried to wipe out all Coordinators with a nuclear missile array, and Patrick Zala, who was preparing to annihilate all life on earth with GENESIS. A life or two was meaningless at this point.
And an example from its sequel is Stella — she stomps through city and wilderness alike in a giant robot, slaughtering innocent bystanders by the thousands because she's driven by a childlike, irrational terror of death, and has been told that if she doesn't fight, scary things will kill her and everyone she cares about. The fact that she's just being used by Neo and Djibril, who are deliberately playing on her fear and pain, makes this all the sadder.
Lord Fezarl Ezelcart, the Big Bad of Mobile Suit Gundam Age, is a married man and was a father. However, the death of his son convinced him that it was high time to root out the weak by waging a war that would eliminate them and create a paradise populated only by the most righteous of humans. Thus began the UE's attacks on Earth Federation Colonies. In the third generation, note the show's hook was that it would not follow an, overall, short war and one group of people as per Gundam tradition, but take place over three generations and nearly a century, fate really twists the knife by having him encounter a young boy who greatly resembles his son... Who just so happens to be a Federation pilot and the grandson of Flit Asuno, main hero of the first generation and the biggest Vagan-hater alive. Ezelcant's son, in his last moments, said that he'd like to be reborn on earth along with them. Ezelcant is convinced that his son got half his wish.
At the end of Fushigi Yuugi, Tamahome unintentionally has a Psychic Link to Nakago's mind revealing his past when he was a young boy, his entire tribe was wiped out, he witnessed his mother being gang-raped, and accidentally killed both his mother and her rapists with his awakened power, only to be sent to the Emperor of Kutou, who raped him repeatedly. As a result, he wants revenge on existence itself for giving him such a horrible life.
Diva from Blood+ may count, although the "Destroyer of Worlds" part only comes about simply because she exists. Chevaliers may love their 'queens' but it seems that Amshel loves power more. Diva went along out of embitterment with the world due to her imprisonment as a child. All that could've been avoided had Nathan simply abducted her and made her a star singer without the whole Take Over the World thing and "make everyone into Chiropterans" aspect of Amshel's and James' agenda. She drops the Woobie part after what she does to Saya's little brother, however.
Yuca from Immortal Rain doesn't know how old he is. All he knows is that, whenever he dies, he's reborn long after everyone he knew before died, while still retaining the memories of each of his previous lives. Over and over again, throughout what seems to be the course of human history. By the point we meet him, he wants to wipe out all humanity just so he can finally die and be able to stay dead.
Shinobu Sensui of YuYu Hakusho began as a heroic spirit detective, but had a mental breakdown after discovering humans torturing demons, throwing his life's work of protecting humans into question — one that isn't helped by his subscription to Black and White Morality. His mind, now fractured into seven split personalities, embarked on a plan to destroy humanity as a way of ending the confusion and guilt, along with a Suicidal Cosmic Temper Tantrum over his terminal illness.
Tsubaki of Mirai Nikki was imprisoned as a sex slave by a cult her whole life before receiving her Diary, and now participates in the Diary game with the stated goal of destroying the world.
Yuno wants to keep the universe in an eternal time loop, forever replaying the Diary game, as this is the only way she believes she can stay with Yukiteru. She wants this so desperately because Yuki is probably one of the only kind people in her life, and her sole reason for living.
Tima of Osamu Tezuka's Metropolis. After getting shot and realizing that she's a robot, she takes control of immeasurably powerful technology and orders the extinction of humanity.
Crona of Soul Eater has the 'destroy everything' part, by way of 'hir' reasoning that everything that s/he fears/threatens hir should be destroyed (for much of the series, s/he understands no other way of 'dealing' with it). Given that Medusa did and still does possibly intend to turn Crona into an Eldritch Abomination in the style of madness incarnate Asura, s/he could feasibly go all the way on this one. Until Our Heroes inevitably defeat hir.
In the manga, Crona is the Big Bad despite being a favorite character of the audience and cast.
Izayoi Aki from Yu-Gi-Oh! 5Ds for episodes 40 and 41. After watching her friend and mentor Divine plunge to his horrifying death, while the only place she'd ever really felt at home in collapses in flames around her, she wakes up from a coma where she relived every single horrible moment of her life all at once to the face of Yuusei, who she already feels conflicted about - and her parents, of all people. Destroying the world from there, though, yes, seems like Disproportionate Retribution, is not that much of a stretch.
Aporia, ZONE, Antinomy, and Paradox, especially Aporia, too.
Chizuru Honda from Bokurano, after snapping due to her love interest and teacher's behavior towards her.
And now, in the manga, Jun Ushiro. HOLY GODDAMNED SHIT, USHIRO. What makes it worse is that it's not his world that he's messing with.
The Melancholy of Haruhi Suzumiya: After going through nearly 15 and a half thousand of the same 2 weeks, Yuki gains emotions and becomes this. Except that she doesn't destroy the world. She steals Haruhi's powers and RetCons reality for 1 year, according to the novels, and 3 years and 5 months, according to The Movie. And she succeeds. And she's stopped by the protagonists. And, for a point in time, there's 4 Kyons and 3 Mikurus.
Homura from Saiyuki: sure, he wants to bring an end to everything in existance, but he's so sweet and vulnerable, and so many undeservedly terrible things have happened to him. His two henchmen fit this trope, too!
Goku. If it weren't for the merciful goddess replacing his broken power limiter when he did he would have killed Rikudo for almost killing Sanzo before Sanzo ever had a chance and before this he goes from adorable little boy to killing machine once his power limiter breaks and he kills hundreds of people upon witnessing his best friend (And only one his age) commit suicide so close that his blood get on him, all so that way he would not be forced to kill Goku and used as a pawn in his "father's" plans anymore. Then later when it breaks again from his overwhelming fear of being alone again and the monks chasing him in the temple just days after Sanzo saved him from the cave he was trapped in for 500 years.
The eponymous Big Bad from Noein is this. It is revealed that he is a possible future of the male lead, who, upon losing his true love in a car crash, started desperately searching the time streams for a way to save her. Unfortunately, he found the multiverse to be full of pain and suffering, and decided to destroy everything and start it over from scratch.
Brandon Heat, or, more accurately, Beyond the Grave, from Gungrave. A nigh-unkillable, unstoppable killing machine capable of destroying armies of super-powered zombies single-handedly with more firepower than some developed nations, by the time he becomes Beyond the Grave, he has forsaken the love of his life because he thought that she deserved better than to be with a ruthless hitman, watched his boss, who was the father he never had, marry her, and been killed by his best friend (he got better) and resurrected by the daughter of his former lover to protect her. He does this by killing all of his friends, including his best friend and his mentor.
Yami Atem from Yu-Gi-Oh! becomes this for a bit in the Doma saga after he loses Yugi - especially during his duel with Haga. Oh, silly Haga, didn't you know that pretending to destroy the soul of a highly protective and emotionally unstable (and once-Axe Crazy) ancient spirit's partner was just asking for a one-way ticket down extreme-pain-and-death lane?
Thief King Bakura might count, given that he became what he was later because he survived and witnessed the gruesome killing of all the people in his village. Granted, they seemed to be a village of thieves, but still, he was an innocent child before this happened.
Malik Ishtar became cynical and evil from his father's abuse of him including a painful tattoo covering his whole back and that's not getting into his alter ego.
Video Girl Mai becomes this in Video Girl Ai, after ending up as a Sex Slave to a boy without a pure heart and going mad as a result.
Broly from Dragon Ball Z is heavily implied to be this in the Eighth movie. The movie heavily implies that his destructive nature, even by Saiyan standards, as well as his overall insanity was the direct result of life-threatening factors from his birth, such as his nearly dying from a stab wound commissioned by King Vegeta simply because he feared his power level, and then having to witness Frieza destroy his home planet. Then his father places a slave crown on Broly and uses him to destroy several planets for his plan to get revenge on Vegeta for what his father attempted to do to Broly and himself.
This was actually invoked by Homura in the third timeline. The two of them have beaten Walpurgis Night, but their Soul Gems are almost completely darkened. Homura's resigned herself to the two becoming witches and destroying the world. Madokadisagrees.
To some extent, Witches in general qualify. A Witch is made when a magical girl lets The Corruption take over her soul gem, transforming it into a grief seed. This usually happens when they cross the Despair Event Horizon. Now remember how many times characters are put into danger or outright killed because of Witches.
Puella Magi Madoka Magica The Movie: Rebellion: Homura finally succumbs to this crossed with Nietzsche Wannabe. We see that she resented Madoka's aforementioned sacrifice, and her Witch form finally emerges. When Goddess!Madoka comes to take her to "heaven", Homura steals her powers and returns Madoka to human form, at the cost of herself becoming the Satanic Archetype to Madoka's Messianic Archetype and eventually having to become her enemy. She then places the entire universe under her control, and maintains the illusion by wiping everyone's memories. And yet...she still feels grief-stricken over the prospect of possibly becoming the series' Final Boss, and is ultimately trapped in a Self-Inflicted Hell.
In Dog Days, the castle-crushing demon prophesized to kill our heroes is really a baby earth spirit, stabbed with an evil sword and forced to eat his mother and then kill everyone around him, until all he wants is death.
Invoked by Wiseman, who Mind Rapes and forces a Plot-Relevant Age-Up on Chibi-Usa to make her believe she has been abandoned by everyone who loved her, thus making her The Dragon and his most loyal follower — the Black Lady. It works for a while, but she's freed from this in the end by Sailor Moon and reverts to her original self.
People under the influence of the Kisenian Flower in Sailor Moon become this. The Kisenian Flower specifically targets people with weak hearts, feeds off their negative energy, then destroys the planet they reside on and waits on the fragments until they find another willing host.
Hotaru. Woobie? Easily the biggest in the series. Capable of destroying the planet and everyone on it? You bet.
Choji Suitengu, the Big Bad of Speed Grapher. His ultimate goal is to die after destroying the corrupted culture of greed that Japan had become, as they forced him and his sister into a living hell.
Kanto from SoilNew Town has had a rough life his dentist drugged and raped him as a child which caused him to feel so ashamed and, well, soiled that he cut himself; it got worse when the dentist reconnected with him in high school and, as proof of his twisted "pure" love, gave him the video of his assault. The shame intensified to the point where he couldn't stand to watch cats in heat and tried to burn down the resident homeless crazy cat lady's shelter (fortunately, he didn't succed). Things seemed to get a little better when he met a nice girl, but just as he was about to have his first consensual sexual encounter, she disappeared from between his legs. No wonder he wants to destroy the world by enlisting the dentist's roughly three dozen unwitting current victims plus a victim by proxy (her rapists were also the dentist's victims) to cause enough anomalies to break reality.
Misa Amane counts, as well. Her parents were murdered and she was about to be killed by the same person that murdered her parents had it not been for Gelus. No wonder she's become so psycho and a huge Kira supporter. It's even more sad when she's interrogated by the police and was asking them to kill her.
Depending on your interpretation, Light may count. The notebook, itself, has been implied to brainwash the owner. This is hinted when he lost his memories, became a nice guy, and then regained his memories and turns evil again. Because of what happened during those events, it's heavily implied that the notebook is the real villain, especially when he sobbed over his father's death (he went from trying to get his dying father to write Mello's name down to sobbing for his father when he actually dies).
Black Mage Zeref from Fairy Tail. Whatever spurred him to go and earn the reputation he has is a mystery, but he's so unbelievably miserable in the present that you just want to hug him. For the love of God, though, donothughim!
ToyMajin of the Fresh Pretty Cure! movie. He was tossed away by his previous human owner and he was filled so much bitter anger, he decided to steal away all toys, then use them to power himself, many of them filled with that same anger. When he captures Usapyon, Love's precious toy bunny doll, it breaks the Cure, making her think that she had the same hatred and drives her to try to make amends... only to find out she never hated her at all. Thanks to the children's love for their toys, Love's able to get ToyMajin to see the error of his ways and sees his true self... a teddy bear. Which she promptly gives to another kid who promises to take care of him.
Scar from Fullmetal Alchemist is one of the few survivors of a brutal genocide which killed almost all his loved ones. As revenge against the government who massacred his people, he becomes a Serial Killer who exclusively targets state alchemists. Fortunately, in both manga and both animes, he gets better.
Pokémon: The First Movie: Mewtwo's motivations for wanting to conquer the planet in the first movie become a lot more understandable when one remembers his childhood, when his only friend disappeared without explaining why he was there and, in the height of his angst, his memories were forcibly erased. Even after his birth, he was taken advantage of by Giovanni until he'd had enough.
Similarly, Moe/Molly from the third movie is a lonely little girl whose mother is long gone and her father is sucked into the Unown dimension. As she cracks under the pressure, the Unown try to make little Molly's wishes come true and transform the mansion into a crystal palace, finally creating an Entei as Molly's father. Said Entei happens to be loyal to Molly to an insane level, kidnapping Ash's mother Delia to make her Molly's mom. And then the Unown's powers start going haywire...
Anatolia Story has Nakia, who used to be a scared teenage girl whose father (the ruler of Babylon) ordered her to marry the king of Hattusa. Nakia was not happy about this, because Hattusa had invaded Babylon not so long ago, the marriage was blatantly using her as a political pawn, and the king was old enough to be her father. She goes through with it and ends up in a strange land, with a husband who has no interest in her at all. Lonely and angry, she ends up vowing to have a son and see to it that he becomes the next king, to ensure her bloodline continues to rule the land. By the time Yuri has arrived, Nakia occupies the second-most powerful position in the kingdom (which she achieved by poisoning Kail's mother) and is using every scheme she can think of to kill her stepsons and husband. As the series goes on, it's clear that she's willing to drive the entire land to ruin if it means getting what she wants, but she's completely and utterly alone the entire time, save for her right-hand man. Even her own son turns on her at the end, thanks to her insanity.
In Doubutsu No Kuni there are five humans who can understand all animal "cries" (animals can't understand each other so predators have no problems killing prey, and prey can't work together to even things out a little, and every night these humans have to hear shrieks of pain and terror). One of them wants to use ancient technology to kill every living creature on the planet because when he killed his own abusive father he saw how peaceful and redemptive dying was; he's also the only one who knows about religion but didn't utilize it to create a death cult, which would have probably been much more effective then suddenly trying to kill everyone without their permission. The surprise second woobie just hates the fact that they she, a clone of someone else, exist(s).