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Brian Clevinger, author of 8-Bit Theater, has claimed that in his comic, the universe exists to hurt Black Mage. Of course, being among the most evil characters in the comic (so evil, in fact, that the symbolic representation of his sins was himself, nothing else being up to the task), he deserves it.
Onion Kid, who loses his parents, multiple sets of foster parents, and an orphanage in unconnected atrocities committed by Black Mage. He gets even by growing up to be the all-powerful Sarda, possibly becoming the force behind Black Mage's own Chew Toy status.
Ansem Retort: Riku, Riku, RIKU. He's been cut in half too many times to count, is pretty much held together only by duct tape, is blamed for anything and everything, and the only reason he has a girlfriend is that she likes boys who don't have the balls to defend themselves.
An unusual example is Laura from Collar 6, who was actually a CONSENTING chew toy.
The Cyantian Chronicles: Khaelis and Marcus, during Campus Safari. Although Marcus does do more to deserve it. Darrik gets gnawed on a little in Akaelae.
In a way, the title character of Dominic Deegan, who often gets hurt for comedic effect, such as when he's punched in the groin by a dwarf who then comments on how the seer didn't see it coming, or when he breaks down in a most humiliating fashion because he lost his candy, and so on.
In Girl Genius, troubles heap mainly on the head of Gilgamesh Wulfenbach. Or his Nice Hat. Wulfenbach-senior was also chewed long and hard.
Robot S13 from Gunnerkrigg Court, at least for the first 14 chapters. He begins the story in a box, shut off, disassembled, and missing an arm, and from there it just gets worse: After being reassembled, he gets possessed, impaled on a sword, imprisoned, and reduced to a CPU because his body was melted down into paper clips. That said, his luck seems to have turned around, ever since Antimony rescued him and Kat started building him a new body.
Paz. So far she only once (when teaching Kat to push her vision and not give up) was the focus of a strip without some misfortune befalling her. She's the first victim of Mort's new-and-improved scaring skills; her hopes to see cows are rather cruelly shot down; then she gets kidnapped. Then her Love Interest has a crush and on Chang'e at that. She takes it all rather stoically, however.
And how could one forget the hilarious Boxbots? Tom Siddell seems to have an unnatural hatred for these poor robots, in that their appearance is always accompanied by frustration, or even facepalming, on the part of the people around them. Even the cast list hates them!
Conrad Achenleck from Hanna Is Not a Boy's Name seems to live to be tortured. He is maimed, killed, reborn as a vampire, battered and humiliated time and time again. And we love every minute of it.
The titular character of Nodwick: How many horrible deaths does a manhenchman have to suffer to get a little respect around here?
Another example: In The Order of the Stick, a pair of Flumphs (jellyfish-like monsters from first edition Dungeons & Dragons, widely ridiculed among players everywhere due to their uselessness) fill this role. Due to their levitation abilities and soft bodies, their purpose in life seems to be to provide the main characters with safe landings.
In this strip, a character falls to their death; in the next strip, there's a panel of the Flumphs, with one saying "Say, isn't there somewhere we were supposed to be?" (Warning! Major Spoilers!)
Another chew toy is the Paladin O-Chul, who suffers abuse after abuse at the end of the bad guys. First paralyzed by Xykon, then catapulted through the air by a Giant Explosion, captured and used as a doll by the child-like Monster in the Darkness, and it only gets worse afterwards.
Jeremy from Platinum Grit is this almost all the time, with suffering and embarrassment being the two defining features of his friendship with Nils. And most readers wouldn't want it any other way.
Kharisma Valleti and Mike Dowden in Something Positive; while both have been shown in a more sympathetic light lately (especially Kharisma, after she was both disfigured and wrongly jailed for murder), they both pretty much deserve what they've been getting. Mike even realizes this, and lampshades that he's paying off a pretty hefty karmic debt. (His last few appearances suggest he has fallen off the reformed-jerkass wagon, though becoming a "real-life" super-hero has helped him tremendously.)
The title character of Crushed, The Doomed Kitty is under a curse that causes her to be painfully killed, humiliated, and left naked... over and over again.
Clover spends the first half of Yet Another Fantasy Gamer Comic being kicked around by three-fourths of the cast and ignored by the remainder. She doesn't even have clothes for most of that time. Her fate takes a remarkable upturn after a while, but she's still waiting for the other shoe to drop.