Sonic is usually the butt monkey in the Paper Mario X series. He gets tortured by water in each story and gets into a really bad situation before going on the team. He even got himself married to Amy, of all people! Amy insits they're husband and wife throughout the third story (even though we know what happened), which really gets on Sonic's nerves, but he's a butt monkey, what're gonna do?
In ToucanLDM's "X Meets My Little Pony" series of videos, Lyra and Bon-Bon are usually portrayed as the butt monkeys whenever they appear.
The Annoying Orange may also count as well, as Apple Bloom did the one thing no knife could ever do—kill Orange.
In The Prayer Warriorsnote A crossover between Percy Jackson, Harry Potter and the Kane Chronicles, Grover is one even more than in canon. He tends to die the mostoften, and gets some of the most painfuldeaths at that, such as getting eaten alive by insects, having his legs broken and getting disemboweled by a spear, or being "demonprocessed" by Stalin and then stabbed in the throat by his former ally Jerry. What qualifies him as this more than anything else is that this treatment continues even after his inexplicable Heel-Face Turn between The Evil Gods Part 1 and Threat of Satanic Commonism.
In Dragon Ball Abridged, Raditz is pretty much this to Vegeta and Nappa. So much so, that they use "a Raditz" as their measuring unit. They can even grow monsters that are exactly the same strength, rendering him completely useless. Needless to say, he's not very happy about it at all.
As of season two, in a commercial for "Spacey's," Raditz is now an equivalent of McDonalds's "Dollar Menu."
On the good guy side, there's Krillin, whose treatment as a butt monkey is tallied on "The Krillin Owned Count."
There's also Yamcha, who manages to disappoint people that have never met him and is ignored by those who have.
Done for comedy in A Very Potter Musical. Ron and Dumbledore repeatedly harp on Hermione for being a know-it-all, buzz kill, and "ugly." She's the only student in the cast who ever loses points for her house (except Harry, once), often for things that other characters are doing, flagrantly, at the same time as her. Harry is the only one relatively nice to her... because he needs her to do his homework, research for the first task, and everything else he's too lazy to do. This lightens up in the second act, though there's still a few jokes made at her expense.
Inglorious Boshtets, a Mass Effect fanfic, has Tali, the Only Sane Woman of her crew of idiots and Jerkasses, getting this a lot, and whenever something crazy happens, at least one of the crew (often Prazza, who's usually the cause of the crazy) will pin the blame on her.
Spike, from Friendship is Witchcraft, is very much a butt-monkey. So much so, in fact, that every character has him listed as a dislike in Dragone Baby Gone, and in Read it and Sleep, Spike falls off the roof and breaks both his legs. After disregarding him, Applejack inadvertently drops a log on him, with other instances of disregard or hatred for him throughout the show.
Krysta from My Little Unicorn . An entire chapter is dedicated to her getting constantly wet in the fight with a water monster.
Reading Rainbowverse has Bonbon, who tends to be put in strange and unusual situations whenever she appears.
TD of The Non-Bronyverse often ends up in all manner of unfortunate situations. Sometimes they're his fault, but more often than not it's because the universe seems to hate him.
In New Champion Evangelion, a fic written by someone who doesn't like Evangelion in general and Shinji in particular, Shinji gets this treatment taken Up to Eleven. He is often insulted and physically abused by the Gary StuAuthor Avatar Ekaj, and in one scene, Misato, while trying to get him to come back to NERV at the train station like in the anime, openly tells him she hates him and only needs him as a pilot.
Mary Jane Watson, the title character of Ultimate Spider-Woman: Change With The Light, really gets burned by this trope. She grew up in a broken home, got kicked out of the house along with her Broken Bird mother by her abusive father when she was 17 and ended up becoming something of a Broken Bird herself and withdrawing into an angry shell. Other misfortunes have been the need to try and find acting and modelling jobs to support herself and pay for her mother's therapy, being sexually harassed by her employers, getting fired from her steady waitressing job for constantly showing up late because she has to fight supervillains as Spider-Woman, nearly being forced to drop out of college after her father deliberately short-changes her college payments, having her grades end up in the toilet and nearly going on academic probation because of her Triple Shifter tendencies, having her backpack stolen by a purse snatcher and getting drenched by a passing car, causing her to lose her dream acting job, attracting a Stalker with a Crush who turns himself into a Psycho Electro to try and profess his sick "love" to her before turning into an even more psychotic Yandere after she rejects him, having a public hate campaign directed against her as Spider-Woman that has several of its members who want to show what a "real" man is, nearly losing another acting job because of her lateness, failing several of her midterm exams after a particularly bruising battle with a supervillain, losing her apartment after she's fired from her waitressing job, and suffering a Heroic BSOD when everything comes crashing down...
In The Emiya Clan, Lancer is summoned up to help take care of the kids because Gil is getting overburdened with nanny duties. He proceeds to last about fifteen minutes before he gets chucked into a wall by Kumako and riddled with bullets by Keiko.
This gets taken Up to Eleven during the Christmas Special where he gets summoned by Zelretch and Alter!Illya as an expendable source of entertainment. Over the course of the day, he gets crushed, impaled, sliced up, burned, frozen, electrified, smashed in the groin, terrified to death, used as a projectile weapon, and several other things. Oh, and when he dies, he gets resummoned immediately, again...and again...and again...and again...