In Hetalia: Axis Powers there is a comic, which later expanded into so many spin-offs it's practically a fandom of its own, known as the World Financial Crisis Gangbang. The cast blames America for the economic crisis... so they (with the exception of his little brother Canada, thank god) gang rape him. And that's not even going into the "America's revenge" fics, where he makes it his priority to torture and murder his rapists in the worst ways the author can think of at the time.
Poké Wars. The authors sometimes get a little too detailed and graphic with the descriptions of what undampened Pokémon attacks do to living beings...
Cheerilee's Garden. In particular, Sweetie Belle's death, although the others could probably spark some unpleasant reactions as well.
Project Mobitropolis, Shax the Raptor's gestalt of Sonic 2 and the backstory behind the SATAM continuity, has an in-universe moment of nausea induction when Prince Martin is deceived by Robotnik and roboticized and subsequently murdered/deactivated, and it proves to be horrifying enough to make Sonic himself puke in revulsion.
Hivefled; the prequel Reprise was intentional Torture Porn, and while the sequel's not so graphic it does carry over.
The Prayer Warriors repeatedly point out that they don't bury the enemy's dead. One has to imagine all those bodies, laying around rotting and getting eaten by scavengers. Some of the death scenes also count.
Virtually any time someone is stoned to death, especially if you're familiar with how it works in Real Life, as it's a long and painful death.
Chiron is killed and eaten by the residents of Camp Half-Blood.
His Shroud infection gives Tails literal nausea fuel, as there are several scenes of him feeling too sick to get out of bed or vomiting into a toilet. His Shroud transformations are just as disgusting. Just to expand, his first transformation includes him ejaculating uncontrollably before his semen turns solid and starts slithering around his body.
Total Drama Equestria, where the cast of Total Drama (who are in pony form at the time) is seen eating grass in Equestria. Now think about this fact. Where the ponies live in Equestria, there are no bathrooms. No toilets, nothing. So... where do you think that the My Little Pony cast go to the bathroom? The Total Drama cast thought about that same question... and quickly spat out the grass they were eating.
Ryuko nearly losing her lower jaw in Chapter 12 is described in very stomach churning details.
Same goes for Charlie Tapatio's demise in Chapter 15 and the aftermaths of Dr. Batty's murders in Chapter 19.
Ragyo Kiryuin and Dr. Richard Batty having (off-screen) sex in Chapter 22.
NES Godzilla Creepypasta: The Organic level. It's a level composed of incredibly realistic, fleshy textures, as well as equally-realistic mix-and-match, grotesque creatures. Worst of all, the boss is a sheep fetus combined with a dog skull.
Just about every chapter of What Lies Beyond the Walls contains at least a mention of faecal matter, and sometimes far more than a mere mention.
The Stronger Evil: Shendu kills Daolon Wong by pounding him into the pavement until the dark wizard is a bloody pulp, and then he rips the remains in half.
In The Dark: While in captivity, Melanie Chisholm is forced to drink blood from a deer, which has been laced with LSD. Considering she seen a deer being slaughter for that blood, it can also be Nightmare Fuel as well.
The Highlander fic The Dragon And His Wrath has a rather vivid description of a deranged immortal using a sharp-pronged metal trident to rip open the abdomen of a captive Methos. The descriptions of blood, organs and waste going everywhere is quite nasty. Also counts In-Universe as the sight and smell cause Joe Dawson, whos in the cell next to Methos, to lose the few bites of food he just ate. MacLeod, the third captive, very nearly follows suit but avoids it.