Bitey of Brackenwood is a complete ass, going out of his way to ruin the day for Brackenwood's other creatures. It is eventually revealed that he acts out of jealousy. He can't stand seeing other creatures happy with their kin, and being the last of his kind compounds this jealousy.
Tom of Echo Chamber. While Tom is an ass to everyone and his excuse for being so is...weak, when he actually admits why he struggles, he shows a scared side. Especially obvious in "Romantic False Lead", when Tom's reasons for loving Porn Girl is that she doesn't threaten, scare, or hurt him.
Both Zaboo and Bladezz from The Guild. The first is a Stalker With a Crush who's just so naive and well-meaning that Codex can't figure out whether she wants to ignominiously boot him out of her life or hug him. The second is a troll and a bit of a Jerkass, but he spends much of season 3 having incredibly nasty stuff happen to him.
Also, Tink, although she's more Jerkass than Woobie.
Zaboo is creepy and horrible with people, yeah, but he doesn't qualify as a jerkass. Even when he does rude things, it's always done with the best intentions and a loving heart. He's just...super creepy. (And a complete Woobie.)
Efeddre of Guts and Sass: An Anti-Epic has a Dark and Troubled Past where he was captured and tortured for nine years. He regularly verbally abuses the people who rescued him, but few feel like they can smack him because it's only been a year since he was rescued.
The Green Goblin from I'm a Marvel... and I'm a DC. The poor guy is always getting beaten up (even though this is Played for Laughs) and the object of his affection is hopelessly devoted to her abusive boyfriend (the Joker). Of course, he does treat his son like garbage.
Jackie from the Jerry series. In the original short, she steals from the protagonist twice. In her own short, she cheats on her boyfriend, beats the shit out of several people, and maces a guy for giving her a flower because he was ugly. And, she gets kicked out of their house, has her suitcase stolen, gets sexually assaulted, gets mugged, becomes a stripper, breaks her ankle, gets sexually assaulted by her doctor, does heroin, etc. The whole thing karmically balances pretty well.
It's pretty mean of Eugene to threaten Matt with a lightsaber, but he doesn't deserve being looked down upon by Matt, all for his nerdiness.
Hugo. It's downright evil of him to knock Matt unconscious, but he doesn't deserve being judged just for being crazy.
The Neopets character Sophie the Swamp Witch is a Grumpy BearSolitary Sorceress, ready to cast spells on any who dare enter her shack and bother her. Her backstory explains why she is the way she is. When she was a little girl, her brother unwittingly brought a curse upon their hometown, which caused all the inhabitants (except her) to mutate into horrific monsters. She was forced to flee into the woods to escape an angry mob, was separated from her family, and lived in isolation for years afterward, all the while desperately trying to come up with a way to break the curse of the town.
The critic himself pointed this out in his editorial "Why is Loki so Hot?", in which he looks up this article to prove a point about Loki of the The Avengers' appeal. Much to his dismay, he found an entry for himself in the trope.
Ask That Guy with the Glasses is obviously more evil than those two for reasons you can find pretty much everywhere, but he had a terrible childhood, is violently fucked up, and you kind have to feel sorry for him when he breaks down in tears for no reason. Then it gets worse when he takes his medicine, and becomes the hysterical but skin-crawlingly creepy persona. It's the better alternative than the horrible, miserable wreck of a man he'd be otherwise.
Upon return, and becoming an Ensemble Cast, other characters fit the trope as well; Hyper's a Tragic Villain stalker, Malice kills people for petty reasons but was sexually abused, and Evilina is daughter of the devil but Critic makes her cry from punching her in the back of the head.
Quite a few specimens fall into this and other Woobie categories... To the point that it's been put up on the "Cliches to avoid unless you SERIOUSLY know what you're doing" list. Especially if "but is really a sad person inside coping by being overly cheery" is their only flaw.
Esau from Stray, who could be described as Adamska's Evil Counterpart. He's a Tykebomb agent of the Patriots who initially comes across as a Smug Snake and does some rather cruel things in his efforts against the protagonists, but his back story is deeply unhappy. And in true Metal Gear villain fashion, his death scene is played for tragedy.
Tales of MU is narrated by one of these, especially with regards to the prejudice and bigotry of which she is routinely the victim, but which she also routinely exhibits to others. To be fair, much of this was taught to her as she grew up by her Knight Templar grandmother. But between the Mechans, the Arkhanites, Winnie, and just about anyone who disagrees with her, she gives as good as she gets on the Jerkass front.
Toki, she started out as this in Time Heals No Wounds II, before her redemption and change of heart. To further drive the point home, she wasn't always like that and was rather sweet, however, deep within the pain from being abused and then neglected (on top of that almost dying of cancer, after it was allowed to reach later stages) eventually poisoned her, allowing her personality to be tainted and turning her into the mentally ill intimidating wreck that she is, making sure no one could ever hurt her again and that she would be one to hurt, in control, and to be betray, just like it had happened to her. The quote below is just a summmary:
Brownie: Toki was once a sweet shy innocent girl who only wanted to be loved, according to Jinx and Spin, but the birth of Frailine turned her shallow, cold, cruel, dominating, calculating, and worst of all, sadistic.
From Ultra Fast Pony, Rainbow Dash. She has an obnoxious personality and likes to gloat about breaking other ponies' stuff. ("Like, OMC, I totally wrecked your house, and I'm not even gonna apologize!") She's also treated like crap by the other ponies, who are very far from being saints themselves, and she is an orphan with a Hilariously Abusive Childhood, and she wants a real family more than anything else. Other characters even note that they're (briefly) torn over how to feel towards Dash:
Rainbow Dash: I just want to be loved for once at the gala. The Choir: No pony likes Rainbow Dash / Because she is annoying / But now I kind of pity her / No wait, the feeling has passed.
Twilight is an arrogant know nothing know it alljerkass, who looks down on other ponies, who she considers ignorant and abuses her adopted son/slave Spike. But, she also has the unfortunate "honor" of being mentored by Celestia, who is very heavily implied to have molested her and later banishes her to a town full of ponies who hate her to the point of having no problem casually insulting her to her face, despite the fact that she saved the world and them multiple times for jack-squat in return and to top it off, she often has to be the only sane mare in world full of crazy jerks.
Twilight: Can I please go one day without any of you guys giving me a migraine? (Rainbow Dash crashes through her home and accidentally wrecks the place) Ok! Five minutes, can I at least have that much?
The Mentally Advanced Series version of Twilight, doesn't exactly have things much better. She is a bigoted, cynical, alcoholic, jerk, who often treats her adopted brother Spike like her own personnel slave and often treats her "friends" with a mixture of contempt and annoyance, often not even trying to actually bond with them, as she's supposed. But, she was also raised by Celestia and spent her childhood going through everything from having her prized stuffed bumblebee torn open to being forced to dissect a dog, because she told Celestia she wanted a puppy. This is not only implied to be what molded her into the pony she is today, but has also left her so emotionally scared that she has a complete mental breakdown anytime she even thinks she might of let Celestia down and at one point breaks down crying after recounting the stories behind the above experiences, before asking her friends if they have any whiskey.. or paint thinner. And that's not even getting into the fact that she is the only sane mare in a land full of jerk asses and at times seems to be the only one that even slightly cares about making better future.
Bitch of Worm has a Hair-Trigger Temper and has maimed and even killed people, but she had an extremely harsh upbringing; her Traumatic Superpower Awakening happened when her emotionally abusive foster mother tried to drown her dog. On top of that, her powers make her unable to interpret human social cues, which left her with No Social Skills. Her Interlude makes it clear that she's very lonely, but doesn't know how to relate to people and acts aggressively because she can't tell whether or not they're mocking her.