Princess Luna from Equestria: A History Revealed when every character, including the Lemony Narrator, seemed to keep on forgetting about her existence. Add onto that the populace's general dislike of her, her social inability to make any friends, and her self-perceived Humiliation Conga after she tried, in which she thought her sister no longer loved her anymore, she fits the bill quite nicely. That all changes when she tries to go Darker and Edgier though.
Tiberium Wars: Sandra Telfair becomes a complete woobie, with her being wounded and captured by the Black Hand for interrogation, then being beaten and nearly raped by a Nod soldier, then having to slit another Nod soldier's throat and being horribly hurt psychologically by doing so. Commander Karrde goes through this too, regularly beating himself up over the deaths of his own men.
Nobody Dies: Asuka. Having her parents divorce early, being rejected from the Evangelion program and treated like shit by her mother in favor of a surrogate son shook her up so badly that she permanently scarred her back and neck so that it might look like she had a contact experiment. Problem is, everyone thought that Kyoko beat her at first. When Asuka confessed, Kyoko got drunk and lapsed into a five-minute My God, What Have I Done?. Even during the school dance (which might very well be Asuka's first real moment of joy in her life), the bitch couldn't resist to hint that there's no way Shinji might actually love her, he's probably only taking advantage of her; the poor girl fell for the trick and got so spooked that she ran away screaming. Rei and Kensuke retaliated by filming Kyoko and her ex-husband going into a storage closet and getting it on, then putting the footage onto Youtube. Even better, Yui completely agreed with their initiative and forbid removing it from the site!!! It gets worse. It turns out that ND!Asuka is so emotionally messed up as to have developed multiple personality disorder. That doll the Canon!Kyoko talked do as if it were Canon!Asuka after literally losing her mind? ND!Asuka talks to it... and it "talks" back.
Team Fortress 2 masterpiece Respawn of the Dead has the Medic as Herr Woobie. To only list a few of the horrible things that happen to the poor guy, he has to put down his pet zombie (is much more heartwrenching than it sounds), has to leave his beloved behind to die in a zombie attack, and is forced to decapitate the member of the team who was most depending on him so he doesn't become a zombie. The poor guy just can NOT catch a break.
Morphic has Gabriel, a Slugma pokémorph who struggles with daily life due to his screwed up biology. Being a mix between a human and a blob of lava, he's basically at risk of overheating and dropping dead. And the chances of overheating heighten when he experiments with his Pokémon side.
Travels Through Azeroth and Outland portrays the draenei as a borderline Stepford Smiler society focused on always remaining joyous and faithful to the Light (not to mention, as empaths who can tell if someone's slipping). However, draenei who suffer great trauma, especially while isolated from their fellows, can end up very unhinged. These draenei are called ashem. While not exactly shunned by society, they are kept at arm's length for fear that their unhappiness will spread to others. Balaa, an Ashem that the narrator meets in Azuremyst Isle, has struck at least one reader as a Woobie: One of the few survivors of a major orc attack, she's battle-scarred, missing a horn, and is painfully ashamed of what seemto the narrator and the readerto be perfectly understandable flash points and minor freak-outs.
From the authors of Mortality and A Study in Regret comes the Children of Time series, a Crossover with Doctor Who and Sherlock Holmes. The Tenth Doctor's woobie status is quickly established in the first episode, having just come out of the events of "Doomsday" and "The Runaway Bride", and Holmes's status is cemented after a Break the Cutie experience mid-series. Watson falls into this category two episodes later, and Beth Lestrade and Sally Sparrow achieve this in the three-part finale. Beth quite possibly outranks them all, being the only character to actually dieand then come back to life.
Nahuatl is the personification of the southern portion of the North American continent. When we first see her, she is a friendly woman who loves her sister. Then, Spain comes across her and beats her, steals her gold, and infects her with diseases that leave her fevered and raging.
Gaho is the personification of the northern portion of North America. At the beginning of the story, she gives birth to twin boys and is very happy with them. Then, the European nations start coming into her land. First she runs into Spain, who tries to force her to give him one of the twins. She fights him off, but is beaten unconscious and has her arm slashed with a knife. Then, she realizes that France and England are both occupying her land, and she is unable to drive them out. No matter what she does, her people turn against her to side with them. And as the story goes on, her children turn from looking like Native American boys to having white skin and blond hair, symbolizing how Gaho no longer has control of her land. She is forced to give one of the boys (Canada) to France, and the other (America) to England, because neither of the children remember her or how to speak her language. The story ends with her as an old woman, living on a reservation and hoping that one day, her children will remember and go back to her. The story was so depressing that the author finally gave in and wrote a sequel, where Canada remembers Gaho and brings America to find her.
Stephanie Salvatore in "To Build A Home", first she has her mind messed with by Katherine. Then develops an addiction to blood living by her own with anguish for every person that she kills. She then falls in love with Klaus only for him to abandon her on multiple occasions and make her forget him and that's just her backstory. In the story she gets raped and is eventually forced to leave by Klaus to save her dying brother.
Bentley the hyena from the Rango fic "Snakes With Guns". He watched his own father's execution, grew up a slave, went insane and tries to mask his angst with a Sad Clown routine. Sometimes he can't take the pain anymore and breaks down crying. At least Priscilla is there to comfort him.
Roger Jr. - Other than being forced out of town due to a house fire alongside his parents and sister, he becomes a thief to support the family. It is implied that hopefully the relationships are perhaps anything but strained thanks to their parents' Big Damn Heroes moment before.
Suzie - Although an otherwise minor character, she seems to be heading that route lately as of now: her older brother Henry'sHeroic Sacrifice has left her shellshocked and on the verge of tears. The implication that she could still be hunted down by those same kidnappers doesn't go well for the little girl.
In Fantasy of Utter Ridiculousness, Once Megas arrives in Gensokyo, it's just one thing after another for Patchouli. Between needing to make a trip in post-storm weather (a combination of heavy moisture and sunshine, the latter of which she canonically detests), almost getting run over by super-sized fairies, getting trapped inside Megas for the duration of its battle against Suika, dealing with asthma aggravation and Coop's refusal to heed her advice... When she finally returns to the SDM, she's stressed out enough to intimidate Remilia and Sakuya into shutting up.
Pikachu of all Pokemon is this in A Pikachu in Love. After spending the entire fic questioning his bond with Ash and worrying that one day Ash will grow up and forget about him, when he finally realizes how much Ash and Co. do love him, he still has to decide between them and his new love Pichi. When he finally does decide to stick with Ash and Co., the scene where he has tell Pichi this is really heartwrenching, especially Pichi had just told Pikachu she loved him not a second later. And then there's the No Holds Barred Beat Down he suffered from that Ursaring earlier in the fic that nearly killed him. It's a good thing Misty finally gave him a hug and told him it was alright at the end of the fic, since by the point the audience would have likely done the same...
Amanda Adams from The Fairly OddParents! fanfic Never Had A Friend Like Me. Her parents are well to do, but totally neglect her, seeing any attempt at interaction with her or spending any cent on her to be a waste of time and money. And they've told this to her face so often that she knows it by heart. As a result her self-esteem is so low, she doesn't feel she should be upset by it, so she can't qualify for a Fairy Godparent, and sees Timmy's parents as perfect . Even Norm feels sorry for her, and a lot of his development comes from realizing that he would torture such a girl in the first place. Her reaction when Timmy tells Amanda the truth about Norm is just heartbreaking. Thankfully Timmy's friendship, and Norm's own growing affection help her get better.
In Horseshoes and Hand Grenades Yuki Jojima gets hits hard. Her best friend (Gentaro) is dead and resurrected by a serpent, her other friend (Kengo) brainwashed and serving him and she is currently blaming herself for not being able to save her best friend because, as she states, all she did was yell "Stop!". To twist the knife further, almost every villain she's encountered will mock her and remind her that she's pathetic and she's not strong enough to save anyone.
In Gensokyo 20XX, just about the everyone is to an extent but the most noticeable ones are Reimu, Chen, Rumia, and Eirin, though in the sequel, Eirin takes the cake in that just about everyone she knows is pretty much hostile towards her, due to the stress, she begins developing anemia and has lost most of her hair to alopecia, and in the end she commits suicide and, wanting to die that badly, she succeeds.
Mega Man Recut has Mega Man. The poor kid just wants to perform science experiments but instead is constantly forced to fight Dr. Wily and his forces, with all the physical and psychological issues that entails. He develops massive self esteem issues and begins to wonder whether he's a human or a robot. He has to deal with constant family problems and his brother tries to kill him on a regular basis. It's very hard not to feel bad for the guy.
Poor Grace Wayne in The Dark Knight fanfiction Question of Honor. First she has to flee her wartorn homeland, leaving the few family and friends that had survived behind, knowing full well she probably won't see them again, married to somebody who is distant to her, falls in love with him while he's in love with another woman and later has to support him while all of Gotham turns against him.
Taken Up to Eleven with John Gage in this series of Emergency! fics. His parents died when he was young and his uncles terribly abused him. During the series, he gets beat up several times,tortured at least twice,mauled by a bear,shot,stabbed,infected with malaria,infected with measles encephalitis,sick several times with other stuff(triggered by losing his spleen in canon,which leaves a person prone to illness)gets dragged through the snow tied to a horse,is temporarily blinded,gets in several mishaps with Roy,...and has a mild autism condition through it all'. The author openly admits that a real person who suffered all that would end up in a padded room someplace.
Megavolt: His best friend and several classmates were killed when Drake/Negaduck burned down the school at prom, hasn't dared to go near his parents since that night since Negaduck promised to kill anyone important to Megavolt, has been trying to stop Negaduck for years before the others arrived on the scene, and is gradually having his memory destroyed by his powers with no way to stop it.
Quackerjack: Mother died when he was born, his father was poisoned by Negaduck, his brother Bobby tried to take care of him when his sanity originally began to fray until the day Negaduck killed Bobby right in front of him and pushed him completely into insanity to the point where it took a lot of work to return him to even a state of semi-stability, lost absolutely anything from his life to the point where the only things he could lose are his new friends.
Bushroot: Originally didn't get his doctorate because of sabotage, had all credit for his work stolen, forced to experiment on himself by Negaduck and turned himself into a mutant plant/duck, and had his two friends killed and was framed for the crime initally. Oh, and it turns out his family are a bunch of criminals who don't associate with the White Sheep of the family and have to eventually leave the city to avoid Negaduck killing them.
Liquidator: Shoved into contaminated water that mutated him into his current liquid state, had his wife killed because of Negaduck, his son was kidnapped and sold off to SHUSH in order to be used for mutation experiments, and the only possible lead that he's found so far was lost.
Ursa from the Avatar: The Last Airbender fanfic Guide Me Home; it's mentioned that she was happy once, but being beaten and burned by her power hungry husband (who later goes on to be the Evil Overlord), murdering her father-in-law in order to save her son, being forced to abandon her children, and going into exile has turned her into a rather bitter and cynical woman by the time the story begins. It gets worse, with her home being burned down, the closest thing to a friend she has being kidnapped by the Fire Nation, her own capture and torture at the hands of Admiral Zhao, and she sees just how twisted her daughter has become under the "care" of Ozai. It takes some time before she even begins to heal, and it is not a quick or easy process, but she makes it.
So far, all the main characters from What The King Loved The Most . Special mention goes to Hearne. He had to see his whole village being burned, lost his adoptive brother who also was his lover, his whole family actually. And he became the Rebellion's leader out of bitterness. Oh, and he hates the current governement because they were "useless". Tiam is also a full-fledged woobie, considering what happened to him in his childhood. To make it clear his father used him as a lab rat for his magical experiments, he was forced to kill everyone is his village, his memories were changed so that he couldn't remember anything. In a flashback in Chapter 7 we have a manipulated Tiam, as a child. Who brutally slaughers a little boy. Ouch. His kind nature also make his suffering worse since he wanted to save Hearne, but had to let him die.
Let's face it: Pretty much all of the old animatronics in the Five Nights at Freddy's fic Brothers Of Circuits could use a hug but Bonnie is perhaps the most notable. As one fan put it in a review: "I feel sorry for them all, but especially Bonnie. He had to experience the same as Freddy, but he actually tried to stay himself. While it was Freddy who should have lead the family, it was actually Bonnie who became their anchor. Bonnie tried protect the family, to keep them together. The friendly and cheery "low fat ice-cream" animatronic was entrusted with the role as leader. He did what he could, being a peace-maker, supporting the others and acting as a lightning rod for Freddy's countless rage fits. He did everything he could until the very end." On top of all this, he has his voice box damaged from Freddy's rage fits and at the end of the story, his face removed. He gets pushed even deeper into woobie territory in the Fourth-Wall Mail Slot. After the fans made Freddy confess his romantic feelings for Bonnie, Bonnie ran off in shock and several fans sent hate mail and death threats to Bonnie, reducing him to tears and making him shut himself off. Despite all this, he's portrayed as a lovable, wisecracking comic relief. Sad Clown much? Let's face it, Bonnie could use a good cuddle, a gift basket of cookies and maybe even a grief counselor.
In the fanfic, "When a Pony Calls, we have Soren.(Not to be confused with the character from the show.) The story starts off with him naively agreeing to an offer made by, what he thought was a random fan, claiming to be Lyra from the show, before his computer explodes in his face and he's suddenly in Lyra's body. Things go down hill from there: He is permanently separated from his family and home, is put through sanity slippage, after a defense mechanism in Lyra's horn mistakes his memories as a parasite, and his human body morphs into a pony too, do to exposure to Equistria's magical environment. That's not even the worst part.
Amy, a.k.a. Panacea, is often treated as a Woobie in Worm fanfic due to her tragic backstory: she was the child of a supervillain who was nevertheless very loving; her father was locked up forever when she was six; she was raised by a clinically depressed adoptive father and a neglectful adoptive mother; and she fell in love with her adoptive sister, possibly due to accidental Mind Rape. In canon, she is rude and abrasive with an extremely black-and-white view of the world, but in fanfiction she is often written as sad and lonely with a friendly personality just under the surface.
While all three of Kiryuuin sisters from Cellar Secrets are woobies in their own right, the youngest sister, Ryuuko, is an even bigger woobie than either of the former two due to being treated like a dirty secret, locked away in a cellar, made to live in a cage, and had suffered very severe neglect and abuse at the hands of their mother. What makes her situation worse is that some people have treated their children like that with said children not recovering very well from that, either.
Star Fall: Being the first Pegasus in modern Equestria, with magic talents, has caused her to be a political pawn in the kingdom for a large portion of her life. Starting with her being taken from her parents (Though at least, by a future parental substitute.) and later, leading to her being forced into an Arranged Marriage by the king, hoping she could produce an Alicorn offspring. Later, she's forced to banish her own parents, so they can't be used to get to her, while they think she's simply disowning them. Then, it's revealed that her mentor/Parental Substitute was a traitor.
Calumn: As a Changeling, he naturally relies on deception to achieve his goals. But, after he starts to become attached to the mother of the soldier he's impersonating and finds a Morality Pet in Trail Blazer, he has a huge identity crisis and questions what it means to be part of his species.
Melody losses everything she cares about, is betrayed by a pony she trusted and looked up to, and is driven insane, after Max Cash manipulated her master into helping him. He then brainwashed her into standing by her dead master, even after he is nothing more than a rotting corpse, and she can do nothing about this but wait for help. After she finally catches up with Max, he bluntly tells her that he does not even remember who she is, before killing her in cold blood.
The Mad Scientist Wars: Andrew Tinker had his dad die, his cousin and first friend leave with no explanation (and harsh enough words that he repressed memory of ever knowing him), at 14. Not to mention said cousin, Desius, being an even bigger woobie who had a... horrific childhood, that ended when he got adopted by Andrew's uncles before having to leave, and forcing himself to deliberately hurt Andrew so as to keep him from getting hurt following him. Let ALONE what happens later in life.
A Very Potter Musical: Draco comes across as a bit of a Woobie in A Very Potter Sequel. Just try to watch the scene where he's writing a letter to Lucius without wanting to give him a hug. Doesn't help that Lauren Lopez has some of the biggest puppy dog eyes I've ever seen....
Scootertrix the Abridged: Luna was imprisoned on the moon for one thousand years, only for no one to even recognize her when she came back. She also has to deal with her Jerk Ass sister, Celestia who constantly makes selfish, reckless, and irresponsible decisions regarding the protection of their subjects, only for herself, to be constantly proven wrong, while Celestia is constantly rewarded with success.
Patch from the Digimon Adventure fic Monkey Business is an absolutely adorable and awkward Gazimon who is often ostracized by the other Gazimon because of his deformities. You most likely WILL want to hug the poor cinnamon roll and take him home with you when reading this fic.
Freya in Aesir: Cross Wars. She is definitely the Butt-Monkey, with all of the other characters making jokes at her expense (though in Azrael's defence, he's like that to everyone). Her Guardian Angel is always disrespectful to her, it's like she has no power in Valhalla. Oh, and all her previous Guardian Angels are dead, and her current one once came really close to doing so. Poor girl.
Advice and Trust: Rei. She lives in near constant pain due to only having part of a soul, she spent most of her life devoid of emotions due to being drugged to the gills, Shinji and Asuka don't return her affection despite being close to her, the one person that has shown romantic attraction to her is a threat to the entire human race just by existing, and she has to keep secrets from her loved ones because they'd die if she told them anything. That's not even factoring in the fact that she gets Mind Raped by Arael. No wonder she's constantly asking for hugs, because she really needs them.
Asuka in The Second Try. Shinji was absorbed into Unit-01 and she went an entire month unsure if she'd ever see him again, she was Mind Raped by the 15th angel for a second time, and she had to deal with her daughter being Ret Goned. All while having to pretend that everything was perfectly normal.
In the show itself, Scootaloo is only hinted to have a physical disability that prevents her from flying and her family status is left ambiguous, but here it's outright stated that her wings are crippled, she's an orphan, and the biggest adult influence in her life is a dimwitted mare child. The worst part? Scootaloo has so little going for herself, when others show concern for her physical health and well being, Scoots brushes them off, because she believes she has nothing to lose.
Maud's social awkwardness is taken Up to Eleven, to the point that she has knowingly deluded herself into thinking she's okay with spending her life alone with her rocks, rather than face how lonely she really is. Maud's also so scared of even trying to change her life for the better, she's Driven to Suicide when she can no longer lie to herself. Luckily, she gets better.
In the Cuphead fan comic from DeviantArt, "Cagney Is a Carnation" by fuyuflowga, Cagney Carnation is going through all the trouble of watching his adoptive flower children lose a casino game and get tortured by the Devil and being forced to sign his Soul Contract and offer his soul in exchange for their lives; being shunned by his peers and forced to scare them and his flower children away to have them find someone else to take care of them; losing everything he's had and almost losing his will to live; having to become a Necessarily EvilDeath Seeker in order to have the sibling protagonists Cuphead and Mugman battle him for the Soul Contract and then reluctantly killing Mugman to spur on his brother's rage (both Mugman and Cagney get better, though); and crossing the Despair Event Horizon when he tells Elder Kettle he's an irredeemable villain (before Elder Kettle snaps him out of it by telling him that the boys have the potential to fight the Devil). After all he's gone through, you really need to hug him so badly. Fortunately, he earns his happy ending and gets better in the end.
The sisters, Satsuki, Ryuuko, and Nui, themselves, in Cellar Secrets, however, the youngest, Ryuuko is an even bigger woobie than either of the former two due to being treated like a dirty secret, locked away in a cellar, made to live in a cage, and had suffered very severe neglect and abuse at the hands of their mother. To really drive the point, she was treated like that for being born during the throes of her mother's mental illness and a collapsing marriage.
Ryuuko in The Outside just simply wanted to experience things beyond her house but it comes at a cost of the life she knew before. What makes this worse that Satsuki's health ends up suffering and she takes a turn for the worse, which will beg the question, as to how she'll cope with her dying. We can assume not well.
Maim de Maim's Nui and, unlike Ryuuko, her life was never good to begin with and just as things were starting to look up for her, she gets knocked down pretty hard when her prescriptions were canceled against her will by her own mother. Damn.
Katara in Cabin Fever. She spends 3 years of her life in the Fire Nation prison for waterbenders, and comes close to breaking like Hama did in canon.