In both versions of Trigun, Vash finally gets Knives to cut the crap after a very long time.
Viral of Tengen Toppa Gurren Lagann is a victim of The Worf Effect instead of The Chew Toy, but the effect is still the same when, after a constant string of humiliating defeats at the hands of the Dai-Gurren Brigade, he pilots Gurren-Lagann with Simon and destroys an entire army by the sheer awesomeness of his presence.
Code Geass had Jeremiah Gottwald, who lost his rank, dignity, and honor after being Geassed by Lelouch, then was crippled trying to redeem himself while fighting against Lelouch, and then was resurrected as a super-strong bulletproof cyborg, willingly joined Lelouch, became his dignified retainer, and might even have a romantic involvement with another of Lelouch's retainers, the beautiful Ninja Maid Sayoko. And in the end... Not only he survives and plays quite the role in the final battle, but he's given a nice and quiet life in the countryside (orange farm included) and an adoptive daughter of sorts in Anya.
For the first part of Macademi Wasshoi, Metallis was the designated Chew Toy. Then he falls in love with Suzuka and, even if he has to find a way to be around her that won't sap him of his power, nothing really bad comes his way again. Whatever the universe had against him is transferred to his former sidekick, George.
In Neon Genesis Evangelion, Shinji spends the whole series thinking of himself as worthless and unworthy of defending the Earth, largely due to his nasty relationship with his father his whole life. The final two episodes are one huge Mind Screw where he retreats inside his mind after being forced to kill his new boyfriend, and slowly comes to realize his relationship with his father is not his fault at all, and he does deserve to be happy. He then finds himself in a pastoral landscape where everyone, including his father, congratulates him on his epiphany. At least, that's one way to interpret what the hell's going on in those episodes.
Then End of Evangelion yanks it, horrendously.
Not really. End of Evangelion is more of an Earn Your Happy Ending counterpart to the TV series' Bittersweet Ending; Shinji goes through a bit more hell, but he gets to spend quite a bit of time with Asuka, and it's strongly implied, if not outright stated, that everyone else can come Back from the Dead.
A less-mind-screwy example for Shinji came in the series, where he lead an assault that stopped a particularly-large angel from destroying Tokyo-3 and NERV. Upon reading the report, and learning how Shinji was by-and-large the person responsible for the day's rescue, Gendo tells him "Good work, Shinji." It's very brief, and done by "Sound Only" video screen, but means the world to a "Well Done, Son" Guy.
a similarly less-mind-screwy example is from the episode where they defeat the angel that was found in a volcano. After they've completed the mission, we briefly get to see Shinji relaxing in the hot-springs afterwards. In the English dub he even says, "this feels like Heaven..." with an almost goofy-looking grin plastered across his face. It's hard not to feel happy for him in the warm-fuzzies sense for that one brief moment. Too bad it doesn't last for him.
Another great example is Asuka. After descending into a downward spiral for the entire course of the series, at the End of Evangelion, she finally learns that her mother really did love her, and decides to kick some ass! Of course, things sorta balance themselves out after awhile...
After several episodes of Garu being forced to endure Pucca's romance, one episode has Pucca accidentally giving Garu the power of astral projection, for once ending the episode with an unhappy Pucca and a happy Garu.
On Azumanga Daioh, Sakaki spends a good portion of the show having trouble making friends because others see her as intimidating, and constantly being bitten by cats whenever she tries to pet them. Eventually, the others (mainly Chiyo) see the real her, and not only does she befriend a wild cat, but it eventually defends her from the cat which traditionally menaced her.
The man in the back of the Ark in Natsu No Arashi spends the entire series asking for salt, and never getting it. In the final episode of the second season, Arashi casually places a shaker of salt on his table. While she didn't know it, that was probably the greatest moment of his life.
Krillin the lesser Butt Monkey does actually get a bone in Z. The man dies three times (four if you count GT), and gets his head handed to on a regular basis. He's vastly outclassed by the Saiyans and to a lesser extent, Piccolo, and is routinely made fun of for his Owned Count. Despite this, he managed to come through and save the day on several occasions— he oneshotted most of the saibamen, he came extremely close to killing Nappa and Vegeta, he played a critical role in foiling the bad guys' plans on Namek until Goku arrived, he sliced off part of Frieza's tail, saving Gohan's life in the process, and he gets to marry Android #18 in the end.
In "Borrowing on Bad Faith", after saving May's Aipom, Jessie asks to use it in a contest. Not only does she get permission, she ends up WINNING the whole thing. They're so unused to winning that when they "steal" the prize, James laughs that they're too stunned to chase after them, not realizing they won the prize (a large amount of fruit) fair and square and gave them no reason to try and get it back.
One Piece's Sanji has endured a great deal of suffering due to being the Straw Hats' resident Chew Toy. Not content to make him a Chivalrous Pervert who generally lucks out with women, Oda's killed his fantasies of mermaids with Kokoro, a fat old lady mermaid; dashed his dreams of getting a bounty with a horribly drawn Wanted Poster; stole his hope to exploit the Power Perversion Potential of invisibility through a villain with a one-of-a-kind invisibility Devil Fruit; and, finally, he was stuck on an island of absolutely hideous transvestites for two years, where he was briefly forced to go native. However, with the crew's arrival at Fishman Island, Sanji has finally gotten to meet real life, attractive mermaids, and they like him. Granted, the nosebleed that eventually resulted nearly kills him, but for him it was Worth It.
Ryoga, the resident woobie of Ranma ½ was given one of these when his virtually perfectly suited and accepting girlfriend Akari showed up near the end of the series.
After thirteen episodes of being Sternbild's Chew Toy, things start looking up for Kotetsu/Wild Tiger in the fourteenth episode of Tiger & Bunny: he manages to finish the season fourth in the rankings, people start treating him as Barnaby's equal instead of his sidekick, his boss stops acting like a total dick towards him, and he seems to have gotten an unexpected power boost. Of course, given the ominous foreshadowing of said power upgrade and the fact that there's still another twelve episodes to go, his luck probably won't last long...
Puella Magi Madoka Magica: Manga only: Homura finally reunites with Madoka in some kind of afterlife. The anime however, condemn her to walking the earth for a long, long time, with no guarantee to ever see Madoka again.
In Axis Powers Hetalia, Romano constantly feels like he's the Unfavorite, compared to his more talented, likable brother Italy. In the 2010 Bloodbath, he finally gets a chance to stand out, when he turns out to have the mark on his chest that everyone was searching for and thus is able to help save the day.
Jagi in Fist of the North Star is a villain with a Freudian Excuse and committed numerous depraved and sadistic acts in the original series. He got what was coming to him. However, in the non-serious and nonsensical DD Hokuto No Ken, he is the forgotten brother of the Idiot Hero trio of Kenshiro, Toki, and Raoh, and when he does appear, it's always to be randomly abused as he tries to eke out a living on the street next to the convenience store central to the show. Even here, he gets beaten up, kicked around, rendered bald, and got impaled on Souther's throne once. He's surprisingly placid, pitifully weak, and serves mostly as a punchline for the show—however, he finally gets a chance to be recognized and accepted in episode eight of the 2013 show in one of the more touching endings present in a Gag Series. (Mood Whiplash destroys this for comedy during The Stinger.)