In the Star Wars: Paranormalities trilogy, this is a common side-effect of Forceless possession for the victims. Aside from gaining a dark appearance and developing glowing red, crystal ball-like eyes, they may also have other mutations depending on the species of the host and intent of the Forceless symbiote. Such mutations may include ExtraEyes(sometimes in places they shouldn't be), extra body parts, an extra layer of skin, or having their internal organs shifted around in a way that makes the host dependent on the Forceless for survival. Also, the host is consciously aware of the mutations, and they are usually painful.
The Death NoteSlash FicNot An Angel has a slightly more realistic (or rather Squicky) take on WingFic that goes into detail about the organic processes involved of growing new appendages out of one's back.
In Robo Bando Hdoug is constantly burned and tortured by Robo Bando to the point his body is a unrecognizable decaying, dying lump of flesh.
In A Madman's Circus is a Death NoteFusion Fic with Vocoloid's Dark Woods Circus the "attractions" at Beyond Birthday'sCircus of Fear are a boy with his face half-blown off forced to dress as a girl, a girl with her eyes gouged out, and a woman nailed to a pole, burned alive and fitted with some sort of torture device in her neck so she screams on command. All of them were at one point just children and visitors stolen by the circus.
The Kin in Hivefledverse are the ghosts of young trolls who died in the Grand Highblood's torture chamber. Of the two most prominently featured, Laneen had the flesh stripped off her arms and an extra pair of horns surgically installed to make her look more like the Condesce's Helmsman, then had her throat cut when she clawed out her own tongue to render herself boring. Her partner Sennir has half the flesh stripped off his head and neck and a gaping gutwound. Gamzee escaped alive, but now has a broken horn and a Glasgow Grin. Various other ghosts have appeared, including a twelve-year-old with a broken neck, a boy with crushed legs, a girl with a severed arm which floats beside her shoulder stump and another girl whose arm is missing completely, and a boy who died from drinking dirty water in a manner the authors tried to be subtle about (most of his guts exited his body in an insalubrious manner).
Happens on a disturbingly regular basis in Fallout Equestria: Project Horizons. Limbs melt and fall off, leg bones melt into jelly (forcing the victim to walk with a set of metal braces), an eye gets crushed in its socket by a rapidly-growing tumor, another character mutates into a writhing mass of tentacles, eyes, and mouths, Blackjack is forced to relive the experience of a pony being forcibly merged with a cockatrice, and a character is hit in the face with a burst of Deadly Gas, melting his eyes and sealing his nose and mouth shut forcing The Medic to cut his trachea open to allow him to breathe.
The experiments' fates after Dr. Hamsterveil captures them in Wrath Of The Damned.
The "Human in Equestria" story You Do (Not) Belong has its protagonist begin growing a unicorn horn after a few days in Equestria. The scene where it begins ripping a hole through the skin of his forehead, which he is then forced to tear off, is Poltergeist-level disturbing, and it looks like it will only get worse from here.
