Church from Red vs. Blue has gone from Chew Toy in Blood Gulch Chronicles to either this or an Iron Woobie in later seasons, due to the tonal shift of the series. As Alpha, he's tortured with endless scenarios in which everyone he cares about dies and he can't do anything to help, so he splits off all the different facets of his personality into other AIs in order to cope. Then, with no memory of this, he's quietly stuffed in a useless backwater canyon where no one ever goes, gets "killed" by his own teammate, loses the woman he loves, and gets killed (for real this time) while stopping the Big Bad. Then, as Epsilon, he meets the woman he loves (rebooted), gets betrayed by her just so she can face-off with the Big Bad, loses her again, gets trapped inside his own memories in a desperate attempt to find her, meets her again, finally realizes he has to let her go in order to be at peace, then gets ripped out of his memories and back into the real world just as he comes to terms with all of his problems. And on top of all that, he finds he's been replaced in his friends' lives by the series' otherIron Woobie, Agent Washington. Flashbacks show Wash as a (somewhat uptight but) generally nice, slightly naive guy. Unfortunately, he's been so beat up, shoved around, betrayed and generally stomped on (usually by his own former partners) that in the present he's a humorless, sarcasticAnti-Hero who readily commits his own betrayals if he thinks it'll secure him some peace for once. If Command has a keyboard shortcut for Caboose's team kills, they've also got one for Washington being shot in the back.
The title character of Sailor Nothing. Let's face it, when one's happiest moment in her life is realizing she no longer is tempted to slit open her wrists with her dad's razor when she wakes up, she needs a hug. Badly.
A lot of abused/outcast characters tend to get this treatment among the users of Survival of the Fittest. For example, in v3 Matthew Wittany tends to receive considerable sympathy from a number of SOTF handlers, primarily because he's just such a complete Buttmonkey and treated harshly by so many of his classmates when he's mostly just looking for friends on the island. Nanami Nishida from v1, despite being insufferably annoying and nearly killing fan-favourite Madelaine Shirohara, got looked upon this way (if posthumously) in retrospect and after people realized just how hard she had it living in Madelaine's shadow. Especially when killing her caused a Heroic BSOD for Madelaine.
Marilyn Williams from the Program spin-off of the same work. Her first thread involved her being beaten up for accidentally walking into somebody, to the point of being made to bleed and having her hair ripped out. This before the 'game' even started.
Dr. Horrible. He needs lots and lots of hugs. Does he ever! Poor guy, it's almost made worse because, even though he's nominally a villain, none of it was really his fault. He has idealistic motives (at least did in the beginning), doesn't want to kill people, only tries to kill his arrogant jerk of a nemesis when he has to kill someone and everyone hates him. And how about the look on his face when he sings "and I won't feel...a thing." at the end of the final number? Hugs all around. And possibly tissues.
Jake from the Minecraft Machinima Newbies has generated a lot of much deserved sympathy among fans for the way he is treated in the show. He shows up as a very friendly player who is using the Mine Little Pony mod to look like a cyan Pegasus. The newbie is afraid of him and Joe tells him to "Just ignore him and he'll go away." After Jake continually tries to get their attention, Joe demands that he go away and that nobody likes him. Jake plays this off like its okay, and is later seen alone in his house playing "The Way it is" on his music box.
All characters in Ruby Quest, more or less, but Tom is a special case even among them. Poor kitty's the sweetest, kindest, the most innocent character in the game by far, and yet he has so far had got himself betrayed and murdered by the woman he thought he loved, forgot about everything until now, had an arsenic poisoning, lost his eye, was rejected by his crush, and finally discovered things of his past he wouldn't have wanted to, including that this new companion of his was responsible of his messy death a while back. Thankfully, he has gained liberal amounts of hug therapy, and all this doesn't seem to bother him as much as it should.
Andrew Tinker of The Mad Scientist Wars 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.
Chic Geek counts as well, especially with recent developments. Note that she's Cousin to Andrew and Desius - seeing a theme?
Also Coach Z, no doubt thanks to his Flanderization from a well-meaning, but somewhat quirky coach into a colourblind, forgetful, perverted moron who thinks he's a mother. In Decemberween Short Shorts, it's been shown that he spends Decemberween locking himself in his locker and drinking nothing but Listerine. Just wait until you see Baby Coach Z.
The 2009 Halloween 'toon has Strong Sad alternating between wishing horrible dooms on his "friends" after not being invited to any of their parties, and staging a surprise party for himself with cardboard cutouts of them. However, even he can't come up with a doom for Coach Z besides being Coach Z. "No sense in beating a dead horse."
Reynold from the Cheat Commandos might fit the bill also.
Parodied with the Strong Bad-created character Lil' Brudder. Explicitly designed to be as Woobie as possible” a hard-working, optimistic, unipod dog "with the heart of a champion” so Strong Bad can abuse others with tales of suffering. However, even Strong Bad feels sorry for the guy. His catchphrase is "I can make it on my own!"
A case could be made for What's-Her-Face in Teen Girl Squad. Since the series is based on off-the-wall (even by Homestar Runner levels) humor centered on the characters dying in silly ways on a regular basis, this is saying something.
New Paper. It's a Replacement Scrappy in-universe; its first five appearances all feature Strong Bad mocking it basically for not being The Paper. It also seems to be rather prone to errors during this early period; in those five emails it comes down prematurely, runs a calibration test when it was supposed to print the Fourth Wall Mail Slot email link thingy, and upon a request from Strong Bad to disappoint him it falls out of the printer. Then in the next email it prints The Paper's striped pattern and perforated edges onto itself to please Strong Bad (who seems to think it's trying to impersonate The Paper, but it "does make [him] feel a little better"). Altogether very Moe. Mind you, a handful of emails later the New Paper aids and abets Homestar's hostile takeover of the email-show niche, which makes it a little harder to sympathise with it. You could see that as the New Paper trying to get back at its verbally-abusive master, but that just makes things worse.
Two, an emancipated golem who, despite her ostensible free will, enters the story with an incredibly flat affect - a sign of severe emotional damage. The cause of this eventually becomes clear; most golems are freed with a full if inexperienced personality but Two was given only one fundamental drive - she wants to do what she is told, whether she likes it or not. This makes her the victim of a horrifying array of abuses, the full extent of which is only implied. Since falling in with some of the kindlier inhabitants of Harlowe Hall, she has gotten better. Still desperately needs hugs, though. About a week of in-story time in, we got to see Two's diary. She needs so many hugs.
From the SCP Foundation, SCP-231-7. Saying anything more here would just ruin how bad it is for the girl. Read it yourself, and understand what the true meaning of The Woobiereally is.
Just to make you feel more horrible: Look at her description. She may be a prepubscent girl. And to make it even more horribly depressing: If the poor girl ever catches a break, it will probably cause The End of the World as We Know It.
Frances J. Worthington III from the Sims 2 story Strangetown, Here We Come is the epitome of woobie. Especially when he is rejected by his crush Tank Grunt, who he had secretly been pining over for months, and has a huge emotional breakdown.
It's even worse because of his eyebrows (Okay, so he's Maxis made- but the author puts them to good use!) which make him look perpetually sad.
Nervous Subject too. Personality-wise, his name pretty much says it all; that, and until Olive sets their house on fire, killing them, the people he lives with make a point of subjecting him to pretty much the worst living conditions they can possibly dream up.
Severin from Fragile. When he confesses his love to Page, Page - who is at this point quite homophobic - rejects him and accuses his love of being lust, even though Severin is later found out to be asexual}}. And then of course there's his incurable insanity and later admittance to an insane asylum. All the while, he has some kind of undiagnosed mental disorder that impairs the way he views the world and reacts to it (Page says that he spent most of the time he knew Severin feeling sorry that he could never be normal). To make the situation much worse, it is revealed in the sequel Perpetual Changethat he was sexually abused regularly by his sadistic aunt starting when he was a child, which led him to develop masochistic tendencies and emotionally scarred him, possibly causing his later psychological problems. It's also heavily suggested that it was an episode of abuse from her that caused his mental breakdown. His psychologist, Dr. Mangum, is also revealed to have given him medication that she knew would only increase his problems. As you can see, a lot of bad things happen to this guy. It's rather difficult not to be sorry for him in some way.
Third place is a tie between Timmy, openly abused and placed in dangerous situations by his Jerk Ass legal guardian who is also skimming his paychecks, and the Sentinel, a demigoddess who accidentally cursed herself into a box to be tortured by demons for a thousand years, was released at the height of insanity by the spirit of Halloween for lulz, and was finally stripped of all her powers and reduced to a mere mortal.
And last but probably not least, we have Liam, who has implied in several places that he's been completely without family since the age of five.
The Gimpi item. It's evolutions before the Star Academy forms scream "Woobie".
Gaia also had an entire Christmas event based on this trope a few years back. The users had to take care of orphans, and get them cleaned up for adoption. The horrible living conditions that the orphans mentioned slid somewhere between Hilariously Abusive Childhood and Video Game Caring Potential. Many users didn't want to part with the orphans once all their conditions were met and the event was over, to the point where they were eventually made into equippable items for your avatar.
Shadow Of The Templar: Jeremy Archer hides it well and therefore it's only hinted at throughout the series, but WordOfGod says he fits this trope quite well. And how!
A few people who watched Salad Fingers think he is just too creepy, and others find him creepy but also endearing. The last episode has a scene where he's crying and some fans said they forgot he's scary because they felt bad for him.
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....
Starkid gives us Duder in Little White Lie. A fairly decent, honest guy is dragged into lie after lie by his pushy, Jerkass sister, then he gets awkwardly shot down by... Lauren Lopez's character, Tanya.
Jay only wanted to look through the tapes from his old college friend's scrapped student film to try and find out why the project was abandoned in the middle of production. The result? Well, being stalked by a tall, faceless abomination turns out to be the least of his problems when he starts losing huge chunks of his memory and people are disappearing around him. By the time he finally meets up again with Tim, he's been living in a hell of paranoia and fear by himself for nearly four years.
Her Robot is just as bad: He was basically built to wash dishes, make coffee and be sex slave, but he has the soul of a poet and is programmed against suicide. You really feel bad for the guy when he's willing to join Dark Nella knowing she will kill him just so he can finally die after being ignored by everyone else. His speech in part 2 of "The Disaster Films of Roland Emmerich" really clinches it.
Waluigi from There Will Be Brawl. Being a Man Child who Wario keeps locked in a pen would be bad enough, but Wario using him to deliver a bomb to kill Red, and Waluigi never realising what he is doing is wrong is what really clinches it.
Fred: Funny or not, sometimes one has to feel bad for that poor kid.
The titular character, Lenny Penguin, in Little Lenny Penguin And The Great Red Flood. He was, until later in the beginning, damned to spend the rest of eternity alone in endless blankness even though he would eventually get out anyway and was destined to do so in the first place. And then, out of pure curiosity, he enters a Time Crack and is sent to an otherwise terrifying Dark World full of equally terrifying Eldritch Abominations. Talk about unfair...
Allison Amber suffers heavily from this trope in Sonichu: The Animated Series, a series of web cartoons that both rip off and rip on the infamous Sonichu webcomic. Poor Allison is depicted as a Beleaguered Assistant who somehow tries to deal with the fallout of the insane decisions Christian Chandler makes as Mayor of CWCville, like his order that the CWCville waterworks circulate orange Fanta soda pop instead of actual water, which is the main reason some part of CWCville is always on fire. Even that's not as bad when Chris essentially forces Allison to clean him up whenever he soils himself, which is quite often. Allison appears to cope with having to clean Chris up by muttering over and over how much she hates her life, while her face has a glazed, vacant expression.
This guy. Stuck in a horrible asylum, abandoned by his family, suffers a severe guilt complex, and has no idea what he did to deserve it all. Oh, and his only friend is a mentally abusive, mildly psychopathic figment of his imagination. With extra Creepily Long Arms. Of course, the fact that he's completely Ax-Crazy by the time he escapes tends to detract from it somewhat.
Legacy -Battlers 2+ introduced Sparks, an upsetting backstory ensues through arcade mode and then you are challenged to EXE in STAGE EIGHT, who in this case is a Hopeless Boss Fight in which Sparks is literally killed by EXE upon losing.
Poor Donnie DuPre from Demo Reel, with his always hopeful smile and tragic doe eyes. 42 but acts far younger, still misses his dead mom, is in an abusive and failing marriage, has such good intentions but keeps on getting crushed, is kidnapped twice and treated as a "pathetic fag" by comment sections when he's abandoned in the woods and is trying to survive in winter, has his present made lovingly by his friends destroyed by SWAG, and dies scared and alone.
The Autobiography of Jane Eyre: Jane, poor lamb. Her life has been extremely difficult, she grew up without proper family and friends, she was abused and expects that it will continue, and she lost her only close friend while she was at school with her. Sometimes she's so down and depressed that it's painful to watch it, and she always beats herself up for being whiny. It's even harder that following Jane Eyre in the book, because it is narrated by the adult Jane who is quite comfortable with herself and controls certain emotions. But Pragmatic Adaptation makes this narrative very real and very immediate. Jane, hang in there!
Welcome To Night Vale: Cecil. Most notably in the episodes 'Station Management' where he cowers under his desk in terror while his nightmarish boss(es?) hunt him in the station. 'Sandstorm part B' where he is clearly distressed after ending up in a horrible parallel version of his radio station, ankle-deep in blood. And in 'Cassettes', where his incredibly woobie-ish and adorkable teen-self is abandoned by his family and finally, confused and alone, is attacked in his empty house. The fandom often exhibits the desperate need to care for and protect him from Night Vale's horrors. To a lesser extent, also Carlos, who is the Only Sane Man in town (as an outsider and a scientist), and rendered hurt, confused, upset and angered by the town on various occasions.