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 (though he was lucky in that his dead self is appropriately male). 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).
Two examples from As Twilight Falls. First we have Luna changing Spike into adult dragon to fight a Discord's minion called Calamity. Then, we have Calamity himself – a skeleton covered with mass of various creatures' bodies sewn together while they're still (mostly) alive.
TD's Ponification in Don't Go In the Everfree Forest, TD. The change is initiated by stepping in a puddle that acts like Conversion Potion cut with Hollywood Acid. When he gets home, he notices his leg's itchy. to quote; "I looked down at my leg. The skin was peeling. Not like 'few-day-old sunburn'. More like 'You can see your muscles.'" As it turns out, as more of his flesh sloughs off, the more ponified he becomes. Twilight has a freak out when she sees him in-between, fingers and toes fusing into hooves, one eye massively bigger than the other, rotting skin dripping off new fur. At one point, convinced he's always been a pony, he peels what's left of his human scalp off.
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.
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.
Eugenesis gives us a lovely description of a Cybertronian "budding" (I.E. their equivalent of giving birth). It happens quite immediately, without the subject being aware they were able to do that, hurts more than anything the subject has ever experienced or imagined, and very quickly involves various parts of their "biology" radically altering themselves simply to ensure the process is successful. Then, once it's done, it happens to them five more times. What's worse is that this is happening to the normally unflappable Soundwave.