Gwen. Unlike David who at least loves Camp Campbell even though he's subjected to frequent pain and abuse, Gwen's not only humiliated by the campers, but she hates being a counselor and has very real anxiety issues from her inability to find another job and the supposed uselessness of her degrees. In "Gwen Gets a Job", it shows just how many rejection letters she's gotten, and when Max finds out, he blackmails her with the threat of getting her fired. She even breaks down crying at the end of the episode because of what her life's been reduced to, and even though David's able to build her confidence back up, she still fails at getting another job at her most recent interview.
Poor Jasper died while he was at camp and can never leave Spooky Island until his body is put to rest, which probably means his parents never knew what happened to him.
Doll Face. Poor thing. Probably comes second to WALL-E on the 'robots you most want to hug tightly' list.
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.
Strong Sad. Though some of his status as a No Respect Guy is fairly amusing, it's hard not to feel sorry for him given the regular abuse, much of it physical and some of it life-threatening, his brothers put him through, the fact that he has no real friends at all (with Marzipan seeming to hang out with him mainly because she feels sorry for him and Homsar being too insane to notice), and his chronic depression—though this is dampened slightly by the fact that he sometimes feels the need to depress everyone else too, mostly early on. One very obscure Easter Egg makes it even worse, by showing that he and Strong Bad once got along.
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.
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.
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.
It gets even worse because of Episode 31 when we learn she was specifically set up to be blamed by Jenna Darabond so she could get Ashely's then-boyfriend Justin and has been The Chew Toy for the whole series. In episode 32 she asks to be left out of the ongoing strife between Mackenzie and Jenna, and Trisha speaks on her behalf. In episode 33, we learn from Ashley's little sister Brooklyn that Ashley has been depressed for a while and their mom is trying to help her.
In a Heartbeat has Sherwin, the orange-haired kid who has a crush on Johnathan, the most popular boy in school. He really gets messed up near the end when he pulls his (Living) heart (Who, in turn, was pursuing him) from him and it breaks, exposing his outing. But don't worry. You know they get together in the end.
Also, Johnathan. After Sherwin gets outed by his heart and exits, everyone in the hallway just stares at him, thinking of him as an outcast for being Sherwin's crush.
The titular character of Nomad of Nowhere: The Nomad is always being persecuted and followed for being the only known magical being in the world. Even when he's trying to use his magic to help others. And because he is what he is, even the few people who actually see him in a positive light have sends him away, due to not wanting to attract any attention from Bounty Hunters and other dangerous and powerful people who want the Nomad.