Woobie / Homestar Runner

• 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 sketchy, 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, as he is treated like a kid rather than a valuable member of the team, and eventually he was locked up by the others for unknown reasons and rarely fed.
• 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. While all four girls suffer many a death throughout the series, What's Her Face is also The Friend Nobody Likes on top of her shared status as a Cosmic Plaything with the rest of the Squad.
• 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.