In Trinites, the members of one of the secret groups, the Devoured Ones, have dark powers that allow them to curse their ennemies when they are wounded. To make things quicker, they tend to scarify themselves right in the middle of combat. Their goal is to gather the body parts of what they think is their lord Cronos. To protect the body parts they have, they will graft it to a dead body, resulting in a horrible zombie that curses you when you slash it.
White Wolf RPG Vampire: The Masquerade has the Tzimisce clan, vampires with the Discipline of Vicissitude, otherwise known as... "Fleshcrafting". As you can imagine, this led to horrible, horrible things. How horrible? Their Antediluvian (the oldest known vampire of the clan) was a cathedral of flesh. And he didn't make the whole thing himself...
Further, in the Vampire Apocalypse "Gehenna" campaign, the Tzimisce clan ends up winning. Because their Antediluvian begins to absorb every living being on the planet into one writhing mass of purified flesh and bone. Unless one of the major characters has enough true faith to call down the hand of God himself at this late point, that's how the world ends.
Don't forget the Nosferatu clan, whose Embrace guarantees that no matter what you looked like before, male or female, from now on you'll be a rat-fanged, bald monstrosity with clawed hands and beady eyes. Some Nosferatu don't mind their own grotesque looks and enjoy the disgust it creates in others- which is why it's not unheard-of for them to seek out beautiful humans just to Embrace them and make them into hideous Nosferatu themselves. Most Nosferatu who do this take a moral stance, choosing only cruel and immoral people they believe deserve to be Punished with Ugly (thus earning them the nickname "Cleopatras", after the beautiful but cruel tightrope walker in Freaks whose murder plot against her midget husband leads the other sideshow performers to disfigure her until she's no longer fit for anything but the freak show herself), but there's always the occasional innocent victim who simply aroused a Sewer Rat's jealousy...
In the newer version, it's a little more complicated and possibly even more psychologically damaging. There are about a billion new and different ways the Nosferatu Embrace can disfigure a new vampire compared to the original- there's still a chance that you'll wind up looking like Orlok, but the odds are just as good that you'll end up some other kind of horrifyingly ugly. And even if you don't? There's still always going to be something about you that makes humans find you repellent and wrong (a lack of human scent, an underlying hunger in your gaze, even just winding up so beautiful that it plunges you straight into the Uncanny Valley).
Meanwhile, those who displease the Chaos Gods are doomed to become Chaos Spawn. The transformation process is described thusly: "The body collapses under the unbearable weight of corruption and is infused with the raw power of Chaos, forcing all manner of strange and disturbing transformations. Chaos Spawn lose what little remained of their original forms, becoming a shifting mass of tentacles and eyes." Yeeeeeeeeeeeuuuuuukkk.
Other servants of Chaos may keep them as pets, occasionally unleashing them in battle (imagine fighting one of those things). Also, it isn't necessary to have displeased the Chaos Gods; sometime it's done for shits and giggles. Such is the nature of Chaos.
Then one has Space Hulk, a boardgame variant of the "Marines vs. Aliens" type, later adopted into an RTS/FPS video game. The information on how Genestealers reproduce (described in loving detail on the Face Full of Alien Wing-Wong page)is Body Horror, made all the worse by certain groups.
No Obliterators in here? Allow me...
The process of absorption fascinates... [unclear] ones body might somehow swallow the item, like unto a serpent or the surface of some [viscous?] fluid. Yet it doth seem a mutual [process]. For not only doth the body absorb the [weapon] but also [doth the] weapon, in some strange way, seem to [absorb] the body... [RECORD CORRUPT] as the weapon becomes like unto my flesh, so doth mine flesh... [unclear] like unto the weapon. Indeed, I trace this [stylus] upon mine arm, and the shape and form of the weapon appears under [my touch?]. It doth not appear in mine hand so much as mine hand doth arrange itself so as to become the weapon... [BREAK IN RECORD] capakhity of mine new form to abkhorb weaponsh ish akhtonishing... [unclear] a whole lakhgun! But I do shtart to lokhe zhe shenshation in mine shkin. Mine jawkh are [hardening?] and mine ribkh are protruding from mine [chest]. Zhey are of a dull, metallic sheen and tekhts show zhey are a mix of [bone?] and shome metal I cannot identify? [BREAK IN RECORD] thsi wil be mmmylsat [RECORD CORRUPT] cannnnnnnnnnnot useth esse febel mahcinsse aaaaany log;ner [RECORD CORRUPT] tothe eyeof the larybinht the hearto fthe maichnettttto the pppplaceo f... metalll... [RECORD ENDS]
Interestingly, Eldar (of all people). If you're a Farseer, you'll slowly turn into a crystalline deposit that serves as a giant digital library for your future generation. If you're an exarch, your body fuses to the suit you have and your mind is slowly absorbed into the suit. Neither this or the Farseer's conditions are reversable. Then there's any sort of mishap with Warpspider jump packs, which can fused you to a boulder, merge you and your pal into an unrecognisable mess, or plant you firmy into the ground while half your organs is turned into plant mulch.
Merging with rocks is also the standard explanation for "Deepstrike Mishaps" (i.e: teleportation failures), with "being delayed and/or sent to the wrong coordinates" as the more family-friendly alternative explanation. Made bloody hilarious by the fact that the rulebook describes it as "they will hardly be of help if this happens".
Any Tyranid biology, especially the abnormal ammo they carry. The Hive Guard's weapon is by far the most horrifying: the living ammunition on the weapon is shot out via a muscle spasm that violently tears its internal organs out, driving it to feed like mad during its last few moments in life, to say nothing less of what it does to the actual target.
Currently the Dark Eldar have this as part of their schtick, especially the Haemonculous Cult:
Haemonculous themselves are already obsessed with rearranging limbs where they shouldnt go (and unlike orks, do NOT possess their adaptive physiology) both on their own body and on their victims and slaves.
Wracks are poor souls so jaded in their daily Dark Eldar life (which is saying something, since all Dark Eldar do is torture, raid, have sex and do drugs) that they actively seek out Haemonculi to serve them, in turn being turned into the same sort of body horror as their master. Grotesques are similar, but they're ones who pissed off the Haemonculous instead, and were turned into gigantic mutants.
Talos and Cronos. These things are giant sacks of flesh and muscle floating around the battlefield in a vaguely human/scorpion shape and are designed to torture and dismember their targets. There is no real origin for these creatures, simply that the Haemonculous created them, which makes it all the more horrifying (given that the Cronos seems to spout new sets of spiny tentacles, one can only imagine where the "material" for these came from).
Scourges are shades of this. They're Dark Eldar Nobles who desire to soar above their brethren as Scourges, which requires them to have wings painfully grafted onto their torsos and their bones hallowed out by the aforementioned Talos. Older ones have gotten more mutated, or have had cosmetic surgery, because they sport beaks and Feathers in place of hair.
Wyches and Succubi, incidentally, are an aversion in the Dark Eldar Army, as they must maintain their beauty in the arena, less they fork over their title due to no one wanting to look at them in the arena.
Even the Kabalite Warriors. They don't wear their body armour normally, it's attached to them like giant piercings.
Lucius the Eternal, a champion of Slaanesh whose killer slowly turns into Lucius from the inside out. Their face remains on some part of Lucius' armour
His description from the Chaos Space Marines 6th Edition Codex
Lucius continued to distinguish himself in the service of his Primarch as the Legion descended into Chaos worship[...]the champion remaind undefeated until he was finally beaten and slain fighting the infamous Lord Commander Cyrius.
Slaanesh was loath to let such a promising protégé slip into Oblivion. Over the next few weeks, the artificer armour Commander Cyrius wore began to warp and change. Cyrius' hair fell out in clumps, and dark lines appeared under his flesh, slowly pushing through his skin as a maze of scar tissue. Soon, Lucius had emerged completely. All that remained of his executioner was a screaming, writhing face, subsumed for eternity into Lucius' armour.
To put this in perspective, mutations, especially from the "Tome of Corruption" splatbook for WFRPG, include things like having your flesh rip itself from your bones and slither away to pursue independent life and condemning you to an existence as an animated skeleton full of bloody organs, being utterly covered in eyes/noses/tongues/nipples, 20 different varieties of Alien Blood, having your facial features rearranged across your head...
Cthulhu Tech has Tagers, people with inderdimesional Powered Armor... which happen to look like Eldritch Abominations. At least they have it better than their enemies, the Dhohanoids, who frequently aren't even humanoid... although they can still shapeshift back into a human form at will.
Tagers don't look like Eldritch Abominations, they areEldritch Abominations. Relatively friendly ones, which are summoned and fused to the human host's body and soul, altering both. Not only do you get the power to change into a biomechanical nightmare, you also are going slowly insane as your mind gets altered to more closely resemble the kind of Tager you had stapled to you.
Dhoanoids are just like the Tagers. Except they're not friendly. And there's nothing left of the human host at all. The body is a meat puppet to be torn off whenever it's not convienent.
Then there's the more "normal" Deep Ones, as shown above, who are not above drug-induced rape to bolster their ranks with human-Deep One hybrids.
Participation in the Rapine Storm, a giant chaotic army marching around Asia in the name of Hastur, guarantees some kind of hardcore bodily mutilation.
And to top off the menagerie of horrors, improper use of magic or psychic powers can open you up to possession, which ends as well as one would expect possession to go in a Cthulhu-inspired world. The government does not consider rogue sorcerors to have human rights, because one cannot be sure they're human anymore.
Most monsters in the GURPS sourcebook GURPS Fantasy II: Adventures in the Mad Lands are former people who have been transformed into hideous monsters either by the land's insane gods or by their own evil natures.
There are a whole bunch of "Body Control" spells that produce body horror effects.
Unknown Armies has the magical school of Epideromancy. Epideromancers gain charges through self-hurt, and use magic to mold flesh like putty. Their minor blast can cause small changes, such as muscular spasms, and does damage. A modified version, Greater Warping, does no damage, but allows you to, in the words of the book, "seal someone's mouth and nose shut, or cause their eyelids to grow together, or melt their arm to their side, or stick their feet together" (censored to protect sensitive stomachs). And their significant blast is called Body Melting. No explanation required.
The school's name translates as "Skin Magic".
Skin divination. Relating to the outer layer of skin, to be precise. See Whatevermancy.
Mind Flayer reproduction in Dungeons & Dragons. They stick a tadpole in your head, which eats out your brain and fuses with the nervous system to take the whole body as its own. And it has tentacles.
Also to mention are the Aboleth, who secrete a musk into the surrounding water that transforms the skin of everyone who touches it into a thin membrane that quickly dies up outside of water, and makes the person to breathe water instead of air. For permanent enslavement, they transform their mostly helpless captives into fish people.
And there's also an ancient powerful entity, Ragnorra, which is the opposite of your average undead creating monster, but actually even worse. Its coming is heralded by widespread mutations and upon its arrival causes endless body horror for every living being in the whole world.
The same sourcebook has Father Llymic, one who does this with The Virus. Turning into a horrific multi-eyed ice-bug monster does not sound like very much fun.
We also get Vargouilles, vampiric outsiders resembling disembodied human heads with tentacles and wings. Should one kiss you, you'll grow tentacles on your chin, your ears will turn into wings, and your head will tear free from your body. Congratulations, you've become a Vargouille.
And the Tsochar, composite beings composed of about a dozen lamprey-like creatures twisted around each other. A Tsochar colony can burrow into another creature and connect to its nervous system as a parasite, or just hollow out its brain and wear it like a suit.
Any D&D character with Willing Deformity or Aberrant Feats, Pseudonatural (or half Farspawn) template or levels in the Cancer Mage or Fleshwarper classes.
Living Walls, which "feed" (and "reproduce"...maybe) by assimilating creatures that happen to come within grabbing distance.
The Slaad, whose alignment was switched from Chaotic Neutral to Chaotic Evil in 4th edition partly because of this fact. They "reproduce" by stabbing or slashing you with a claw, injecting eggs into your flesh as a side-effect. If you don't get healing magic or surgery, the eggs hatch and the Slaad "tadpoles" chew their way through your nervous system to your brain, devouring it and then breaking out of your skull to grow into new Slaad adults. There's even a Slaad Demon Prince, whose layer of the Abyss is like a gargantuan, sprawling array of pestilential entrails flocked with screaming slaves sewn into the walls — said "Prince" is a giant "female" Slaad, so bloated with eggs she can't even walk and instead drags her swollen body through the rotting, pus-oozing fleshy tunnels, implanting eggs into any slave that catches her attention.
The chestburster egg was only half of the reproduction cycle, used by red slaad to birth blue slaad. How do blue slaad reproduce? Their bite carries a disease known as slaad fever that warps your flesh (making you increasingly sluggish and clumsy via Dexterity damage) and eats away at your sense of self (Charisma damage) until your increasingly malformed body becomes a red slaad that remembers nothing of its previous life. And will then go around laying eggs in people. Yay!
An oldie but a goodie, the Yellow Musk Creeper and Yellow Musk Zombie! The titular Yellow Musk anesthetizes most humanoids very efficiently, and the self-mobile vine then plants a seed in the victim's skin. The seed germinates and kills the victim, taking over their body to WALK TO A NEW PLACE TO GROW.
The Spelljammer setting had outcast Elves based rather obviously on Guyver. Player characters could find a 'seed' that, if touched on the trigger point, would explode and envelope them. It would kill any orc, goblin, troll, ogre, or similar creature outright. If you were human or part human, it might merge with you, and would always merge with any kind of elf, turning the affected character into a Guyver-style biomechanical warrior (including the ability to hide the exoskeleton away internally when not in combat). (In setting, these were applied to volunteers during the Unhuman Wars. After the end of the Wars, the survivors were ostracized from Elven society, in a rather heavy-handed Vietnam War Vet reference.)
Those who displease the Drow goddess Lolth are transformed into driders, horrible human/spider combinations. (However, in the 4th Edition, this was changed via Retcon, making this transformation not a curse, but a reward for exemplary service. In fact, that makes sense in way, as it seems strange that Lolth would punish a drow by making her into a more powerful creature and transforming the subject into her own likeness.)
In the Ravenloft campaign, Yagno Petrovna, the darklord of G'henna and high priest of Zhakata can transform people into mongrelmen, misshapen, deformed, ugly creatures. He usually does so to punish his subjects for real or imagined crimes of hearsay. This doesn't work on anyone who does not believe in Zhakata's existence, so that means most Player Characters (and pretty much everyone not native to G'henna) are immune, fortunately. (Zhakata is not a real god, existing only in Yagno's deluded mind.)
The Despoiler of Flesh is a powerful evil artifact first mentioned in the epic Planescape module Squaring the Circle which later appeared in The Book of Vile Darkness. It can basically inflict this sort of condition on a victim, and is limited only by the imagination of the user. (But if the reshaping is anatomically impossible, the victim dies, collapsing into a pile of goo; owners tend to be sadistic creatures who torture slaves and prisoners with it.) Worse, the Despoiler is probably the most disgusting magic item in the game; it's a wand made of human tongues which constantly drip saliva. To recharge its power, the owner has to sew more tongues onto it.
The Liber Mortis includes the Mother Cyst feat, which gives the user an, optionally visible, swelling that enables them to inflict horrific cysts on creatures. They can then use said infection to track or scry the targets, dominate them, or inflict painful or lethal swelling. At the highest levels it can turn into a Chest Burster or outright devour their soul. Though if the target is killed in this way it then absorbs some of their tissue to become an undead monster. This can be a good or bad thing, depending on whether you can control undead.
The Nightmares from Don't Rest Your Head. A fusion of Victorian-era societal roles and Dali-esque mutations.
The Z'bri from Tribe 8 are the masters of this trope. Pray that they don't catch you alive.
Exalted gives us many a case. Let's start with Casteless Lunars. Due to spending several centuries hiding out in the Wyld, the very act of being Exalted as a Lunar means you get infused with some of its chaotic essence; you need to receive moonsilver tattoos (and thus, a Caste) to resist its influence. Those who don't risk losing a portion of their control every time they shapeshift. Eventually, they begin to accrue permanent Limit, and with it, the really weird mutations. In time, the Casteless Lunar may well become a Chimera, utterly inhuman and utterly insane.
Canon example Chimera, Echinna, was imprisoned in the Wyld for decades (or was it centuries?) and has, as a result, completely lost control over her shapeshifting powers. In her illustration, she has (hidden for the sake of readers' appetite) bony appendages for hair; three eyes on her forehead; three breasts of different sizes; feline striped furs on her right side; righ—a leg of a mantis, an ostrich, and... one that is a whole squid with a moose's leg emerging from the tentacles; a reptilian tail with a whole upper body of a lizard at the end, which is vomiting a tail of a tadpole and a raptor's talon; a leather butterfly wing and a mess of bird's wing bones; a left arm with saurian talons; and two right arms, one of which is an erroneously grown cluster of tentacles and another which is a wolf fetus. She is covered in random, half-grown body parts (such as eyes) and bound with a braided length of intestine. The full glory/horror of Chimerical existence can be seen here (NSFW, by the way). While such a random, impossible arrangement of mismatched body parts can be a form of Chimerism, some Chimerae go the other way — one suggested example is a pool of body fluids that stares at you.
Also, a lot of stuff to do with the Infernals. We're talking people who can self-induce hyper-speed, tumouriffic-skin-peeling-off radiation sickness and only get nastier. (Details on Lillun in particular wouldn't be good for you.)
Buuuut, since we're sadistic bastards, here it is: Lillun was a young (about twelve-year-old) who was sold to the Yozis by her mother and transformed into a phylactery-womb to hold the Infernal Exaltations when they're not currently in a mortal host. This has had the dual effects of shattering her mind and mutating her body into a massive, bloated, diseased *thing* covered in diseased flesh upon which various unnatural orifices randomly open and close.
And anybody who goes into the Wyld is automatically dealing with a strong risk of this.
Voidtech Charms for the Alchemicals tend to involve modifying their forms and installed devices with a horrifying blend of machinery and meat. This would merely be "bad" if Voidtech didn't by its very nature inflict a form of psychosis.
In KULT, this can happen to you if your mental balance falls low enough. Your new look will tend to reflect your soul.
The nastier Exsurgent virus strains in Eclipse Phase deliver this to their victims. It is strongly recommended that you don't end up with said strains. We mean seriously, bullet-through-the-stack recommended.
Dragons in Iron Kingdoms can warp, if not kill, their surrounding with their blight, but the most visible warping occurs within the ranks of Everblight. Mutations among his warriors include scales and pointy spikes protruding from their skin, change of human-like legs into wolf-like, up to growth of wings.
FATAL is a tabletop game with too many issues to possibly list, but body horror is right up there. One egregious example is a miscast spell can leave a spellcaster afflicted with a massive, grotesquely swollen nutsack for a random number of days. This game is infinitely worse for women and female characters, too.
In Werewolf: The Apocalypse, fomori are formerly-living beings (generally human, although the rules potentially allow anything to be corrupted) that get corrupted by the Wyrm. This transformation can be rapid or slow, happen whether or not the poor victim even realizes it, and the poor victim may find themselves press-ganged into a cosmic war where they still have the mindset of an ordinary human and their best-case scenario might be getting ripped apart by werewolves. And the transformations can be many varieties of horror - literal worms bursting from their insides, acid pustules growing all over (even their insides), painfully growing spikes from anywhere on their bodies, other body parts rotting off... there's no limit. The supplement detailing the many types of fomor (published by the "adult" line Black Dog) went into detail, for example, as to how a normal human becomes transformed into The Worm That Walks.