Erika Hayasaka from MegaTokyo is cool, calm, sarcastic, and quick to inflict violence on anyone who violates her personal space. At first thought to be the only one in the cast who wasn't awash with neuroses, she eventually turned out to be possibly the most damaged of them all. And it was the title of one of her albums.
In Blood Bank, most Art count as this: humans selected at a very young age to be raised as slaves for bourgeois vampires, often for sexual reasons. If they're "lucky" enough to escape being drained of blood by their masters after outliving their usefulness, they usually end up in the slums, unable to readjust to normal life. Special mention goes to Humpty Dumpty for being treated with drugs that prevent him from ever aging.
Jillian Zamussels turns out to be a Broken Bird, among other things, due to being the princess of a destroyed kingdom that she never wanted in the first place, in addition to massive amounts of torture, Mind Rape, and failed attempts to Screw Destiny.
Her lover and torturer (yeah, it's that kind of relationship) Wanda isn't better: her backstory, explored in the "Inner Peace (Through Superior Firepower)" stories, reveals just how much she was broken, repeatedly, during her first turns of existence, slowly turning her into the ruthless and Fate-abider character she is nowadays.
Bunny Velvetino. Her voice was taken from her by the Great Minds after she revealed Thinkamancy secrets to her lover, Prince Ponzie. It is later revealed that these secrets involved literal Mind Rape from Doller Bill, who would rape a doll that she was mentally linked to. She is also implied to have had a hand in Ponzie's death when he tried to seize the throne, having to choose between Don King and Ponzie.
Mary Posa of Henchgirl: A combination of her superhero parents discounting her and her mundane super-strength and the circumstances of her having to survive on the mean streets of Crepe City turn Mary into a fairly skilled criminal. However, crime takes an emotional and physical toll on her, making her feel unfit to be among her family and friends, and unable to navigate the legitimate world. It gets worse after she is injected with evil serum and ends up getting her sister in crime, Coco, and her quasi-boyfriend Fred killed after Mary kidnaps Amelia in a jealous rage and attempts to kill her.
Faye — though she subverts the Freak Out, she makes jokes about it while she's in obvious pain from bringing it up, and chooses to tell Marten beforehand. Still counts, though, because she is pretty broken. After finding out the whole story, Marten is careful to explain the situation to her next potential boyfriend.
Angus: Wait, how do I know any of this is true? Maybe you're still holding a torch for her! Marten: Dude, when a park ranger warns you about bears, it's not so he can keep all the bear hugs for himself.
More recent issues indicate that Dora may also be one, particularly regarding her relationship history and trust issues with Marten.
Considering recent developments with her character, Tsukikomight be this - or she might just be crazy. She says that she "likes" the undead because she thinks that living people are the real monsters and therefore the undead, as their inverse, must be good. It is, however, unclear whether these opinions come from personal experience or not - if they do, she's probably this trope, and a good deal more sympathetic than she had been previously. Which wouldn't be surprising, as a lot of villains tend to have a dimension of sympathy. (Except the Big Bad himself, by admission of the creator.)
MikoMiyazaki could be interpreted as such as well; she was orphaned at a young age, is severely socially awkward, and her only friend is her horse. One could imagine a lonely young girl with poor social skills adopting a rigid black-and-white view of the world as a means of emotional defense - only making things worse, as her narrow-mindedness and arrogance drives people even further away from her.
Galatea ("Golly") in The Inexplicable Adventures of Bob!. is much less of an emotional disaster than she once was, but she still tries to project an air of competence and experience far beyond what she actually has (even if she is a genius).
In Homestuck. AradiaMegido. The poor girl is so broken by the time the game starts that she's forgotten what emotion feels like, which makes her ascention to God Tier all the more heartwarming.
Bathory of Crepuscule seems to be this, as revealed in more recent chapters: For hundreds of years, she's been searching for a surviving relative from the extermination of the pureblood succubi. Thankfully, she finds Angela, her aunt, and seems to be getting better because of it.
Lei'ella if Inverloch puts on a ruthless facade and uses Spock Speak to intimidate people in her capacity as a thief-catcher, a job which she admits usually results in her killing someone. She's cynical about Acheron's motives, and refuses to believe the thief Varden has any capacity for goodness. This is because she's an elf "afflicted" with mortality and exiled when she was twelve; since then she's had to hide her race because she's invariably been rejected by prejudiced humans.
Ophelia Banksly from Riverside Extras. She's strong, clever, sexy, and poised - probably the most skilled gangster in the Roses apart from founder Ma Oceana. She also has a Dark and Troubled Past that left her with physical scars and a tendency to dissociate, can't show weakness most of the time because of the racism and misogyny she faces as a black woman in a majority-white gang, refuses to confide in anyone (including her best friend Derry and lover Simon), and is younger than her mature, sophisticated demeanor projects.
In Rascals, this appears to happen to Reiko when Skye calls it quits on their relationship as evident on this page and future pages of this particular arc.