Advance Wars: Days of Ruin. Creeping Derangea causes flowers to grow under the skin and then break out. Painful, but it only infects people under 20. Initially.
The main plot of Agent USA consists of fighting against an experiment with a TV set which had Gone Horribly Wrong and is now turning every citizen of the United States into mindless, walking TV static. The worst part is that this can happen to your character, and instead of ending the game, you just wander aimlessly forever, having lost your mind and turned into fuzz.
Alter AILA Genesis: The prisoners near the core of Orbital Prison may or may have not been mutated by the Nightmare System. Trauma is the most notable example and he transforms into a plant like being when he takes enough damage.
Amnesia: The Dark Descent has this in a lot of ways. For example, the Gatherers. Their bottom lips are stretched down and fused to their chest, turning their mouths into gaping maws that never shut. And they used to be human.
In Ancient Domains of Mystery, the corrupting radiation, slowly affecting the inhabitants of the world, causes several stages of mutations. These include ten extra eyes, gaining poisonous hands and the transformation of feet into hooves, just to name a few. These have an actual effect on gameplay. Becoming too corrupted will eventually dissolve you into a pile of pure Chaos.
Thought seeing the chestburster explode out of John Hurt's chest was bad enough? The second level of the Alien campaign in Alien vs. Predator 2 starts out in the host's torso, with you as the chestburster. No prizes for guessing what you have to do.
The Sauroid enemies in Arc Rise Fantasia are all revealed to be humans in the midst of transforming into feldragons, the same creatures the protagonist spent his entire life slaying.
In Borderlands, the Badass Psycho has one tiny, almost vestigial left arm, and a heavily overdeveloped right arm.
The Badass Psycho reappears in Borderlands 2, and gains company. A relatively rare enemy called the Lab Rat has been driven insane by medical experiments, gaining glowing eyes from which it can shoot lasers. More commonly, bandit troops called Goliaths are always seen wearing some sort of headgear; if this is shot off, their face peels back over their skull, allowing their spine to elongate and thrust it clear out of their mouth. A player can actually see their face wobbling around underneath the swaying, gore-coated skull as it scans for victims... not with any great ease, since the Goliath Turns Red when this happens and goes berserk, attacking much more viciously than before. A Goliath variant called the Caustic Goliath starts vomiting acid in this state as well.
A trailer for Bioshock features the first-person protagonist in hand-to-hand combat with a Big Daddy Bouncer. He injects himself with an EVE plasmid into his arm, which causes the limb to apparently rot into a mass of suppurating sores, whereupon a swarm of bees crawls out of the holes in his arm while he screams bloody murder. And then it turns out this effect is in the game proper...
In addition to your hand becoming a living beehive with Insect Swarm, equipping other plasmids is just as disfiguring. For example, the Fire, Ice, Lightning trinity of plasmids cause icy spikes to burst out of your hand (yes, with traces of blood), your hand to be covered with horrific burns and your veins to vividly glow with electrical energy, respectively. It's subtle, but if you look at the "pheromone" plasmids like Enrage, you can see your hand is covered in pus-filled blisters, implying the "squishy ball" is actually a clump of your own tissue.
The disfiguring effects of Plasmids have become so iconic that they remain in Bioshock 2 and Bioshock Infinite, despite the fact you play as a no-longer-human Big Daddy in the former and they're an entirely different gene-booster called Vigors in the latter.
Infinite has a few very notable varieties of its own, especially since receiving a new Vigor prompts a brief cutscene in which you get a good look at some of its side-effects: for example, "Devil's Kiss" causes your hands to burn from the inside out - right down to the bone; the idle animation to "Murder of Crows" has your hand sprouting feathers and your fingernails growing into claws; "Bucking Bronco" shows bloody cracks forming in the skin of your hand, flesh dropping off in petrified clumps; "Shock Jockey" results in electricity-conducting crystals bursting out from under your skin; "Return to Sender" slowly peels away the flesh of your hand and coats your finger bones in a black, metallic substance; even the comparatively benign "Undertow" sees pulsating octopus suckers and barnacles forming on your skin.
Overuse of the miraculous gene tonics and "plasmids" that grant these special abilities leads to a different kind of body horror — many of the Splicers encountered in Rapture are visibly deformed, in some cases featuring huge tumors growing out of their misshapen and twisted faces.
Though the Splicers shown in-game are undeniably horrific — the most notable being the Crawler of Bioshock 2 — there are many Splicer designs that just didn't make the cut, though they helped in getting Bioshock made. There was Yam-Hand, a big, hulking, blue-collar type with one giant, potato-esque hand that he was forced to use almost like a club/cane/crutch, to the point where he stood like a gorilla. There was a man whose skin had begun to melt off of him, revealing various innards and bones. And there were various parasite-infested people, who weren't even people anymore. They had been taken over by insects, who had grown inside of them, and then, eventually, OUT of them. They were gigantic insects with various limbs, faces, and articles of clothing protruding from them. "Squick", indeed.
There was one Big Daddy design that was "no fun to fight" that had Combat Tentacles growing from its wrists and humeri.
The Big Daddy-fication process is beyond horrific (skin melted off, grafted into a diving suit, implanted with a voice box, mind wiped, etc.).
In Breath of Fire: Dragon Quarter, when you get your D-Counter to 100% and give up, a game over scene will play in which you get to see Ryu's silhouette on a red background getting brutally, mercilessly torn apart by Odjn bursting out of his body all while hearing Ryu's screams of agony. Pretty unusual for a JRPG to actually kill the main character, let alone in such a violent way.
One enemy type in Bullet Witch is misleadingly called grubs. They're actually what happens when the ghosts Screamers spew possess a person — a grotesquely distorted human with a bizarre, bloated head, that moves in a freakish way, and attacks you by biting you with its ribs and spewing fire.
Captain Blood is a videogame too old to evoke actual feelings of body horror, but the novella included in the manual, explaining the premise of the game, more than makes up for it. The main character of the game is a game programmer named Bob Morlock, who proceeds to create a space exploration game so realistic, it becomes real. Bob is teleported aboard the organic spaceship he created, where he is accidentally cloned 30 times after a hyperspace jump. The book then explains in detail how Bob's organs start shutting down because of the "vital fluid" he lost when he was cloned, and he needs to replace them by mechanical substitutes, gradually turning into a robot. But that is only a temporary remedy, because the goal of the game (stopping Bob's body degeneration) can only be achieved by killing all the other clones and absorbing their vital fluid.
In City of Heroes, there is the Devouring Earth, creatures made of plants, stone, and flesh. Their goal is a world without humans. They achieve this by taking humans and mutating them into more Devouring Earth. During the Underground Incarnate trial, you get to see the Praetorian strain of the mutagen at work - people (and robots) with bulbous blue tumors sticking off of them as they begin their transformation into Devoured, gigantic, tentacle-faced, claw-handed monstrosities that, at one point in the game's past, could summon Swarms (essentially, mutated bees) from a hole in their hands.
Earlier, there is a story arc devoted to helping a woman who has caught the amorous attention of the leader of the Devouring Earth, Hamidon (a four-story tall amoeba). A fair portion of the story arc involves keeping her away from the Devouring Earth to prevent them from infecting her. The second to last mission is prefaced as a rescue mission, as the Devouring Earth broke into the safehouse where she was being kept. When you find her, she has already begun mutating into Terra, a Devouring Earth broodmother. The final mission has you capturing her, with unfortunately little hope of a cure.
There are also Arachnoids, creatures created by Lord Recluse through attempts to mimic his Incarnate powers on rank and file soldiers. They have varying levels of retained sentience, some being little more than mindless monsters, with many others still being intelligent enough to lament their fate.
Clive Barker's Jericho is utterly rife with this. All of the monsters in this game were once human: upon becoming trapped in The Box/The Pyxis and succumbing to death, they are "assimilated" by the Firstborn. Upon returning to life, they have transformed into grotesque parodies of their former selves. Some of the more extreme examples include Arnold Leach, who has transformed into a winged creature with his eyes being forcefully held open by what appears to be thick leather straps punching through his eyelids and scalp; the Crusaders, who have replaced several of their limbs with assorted weaponry and nailed their own armour to their flesh, and the Corpses Behomoths, who are essentially a mass of human corpses held together by a collective mind, formed into the shape of huge, crawling creatures, with a metal mask held onto their "faces" via strips of skin, through which they spit toxic corpse chunks.
In Clive Barker's Undying, Bethany got her final revenge on her brother Aaron by chaining him inside her private dungeon and letting rats eat him alive, removing his jawbone so he couldn't scream. Which also qualifies as Artistic License - Biology, since removing someone's jawbone does not affect his ability to scream - the vocal cords should be removed for it. As a matter of fact, he could probably do nothing but scream.
Clock Tower: The First Fear: has a severely deformed ten-year-old named Bobby, a mummified corpse you find in the trophy room, and a huge, deformed, purple infant-looking thing who is the twin brother of Bobby.
Who can forget the squiky moment in The Crooked Man when you mean the title character and he twists his own neck before pursuing you. (shudder)
The Egg-burdened in Dark Souls. These poor guys have giant eggs growing out of their backs that are so heavy and huge that they can't even walk and are reduced to crawling. Despite this, most of them actually don't mind their situation seeing it as proof of their devotion to the mutated Daughters of Chaos. Many of them also carry Egg Vermifuges which can cure their condition — it's entirely their choice. If you make one hostile, it will attack you and plant an egg in your neck that will eventually cover your entire head. It's actually in your best interest to do this at least once, since the Egg-burdened NPC Eingyi will interpret your condition as a sign of devotion to the Fair Lady. He will then offer you an Egg Vermifuge and sell you the forbidden Pyromancies that the other Pyromancers exiled him for creating.
The Necromorphs of Dead Space are alien parasites that infect dead bodies. The infected corpses reanimate and start growing all sorts of disgusting appendages to kill the player with, such as bone claws and tentacles.
But among them, the Guardians and Dividers fit into this trope the most.
The Bosses should be also noted. They are fused from many human corpses! Needles to say this corpses are clerly distinctive. Hell, even some kinds of basic Slashers seems to be made from two fused humans.
For an added extra dosage of sheer WTF: Unitologyworships these things! Their whole religion is deifying the instruction manual that humans used to create the Necromorphs in the first place ( the Black Marker was an alien artifact, but humans decoded the information on it and, in a Species fashion, the genetic code for the Necromorphs was amongst that info, while the Red Marker was also made by humans using reverse-engineering of the Black Marker), treating being turned into a Necromorph as the key to becoming a "divine, immortal being". Needless to say, many of the more sane Unitologists started having doubts about their beliefs when actually confronted with the reality of the Necromorphs.
Bonus points goes to the fact that during the development of the necromorphs, the dev team had a "horror" binder full of victims of car-crashes, bear attacks and various under unpleasantries.
The Unclean Beast of Demigod. Grotesque as it looks, you also have to remember that this...thing...grew inside a human womb. An ordinary woman had to carry and give birth to this, completely ignorant as to what was growing inside of her.
Dragon Age: Origins features something like this with the abominations. While the player isn't given a chance to witness the transformation due to a glow effect, the way demons take over mages in the game universe results in a rather gruesome version of a human (or elf).
Darkspawn in general qualifies as this once you learn that they were the various races that populate Thedas, only mutated beyond recognition by the Darkspawn taint. The well-rounded hurlocks were humans, the numerous genlocks were dwarves, the stealthy shrieks were elves and the massive ogres were qunari.
Worse yet is the Broodmother boss fight later, which lets the player know before fighting it that the gigantic horrific boss was once a dwarf woman. This transformation is given as the explicit purpose for which the darkspawn even abduct mortal women rather than killing every last of them.
In the finale of Dragon Age II, First Enchanter Orsino snaps after seeing so many of his fellow mages slaughtered by the Templars. Having crossed the Despair Event Horizon and wishing for nothing but revenge, he sacrifices his principles and his humanity (technically he's an elf but still) by using Blood Magic to merge with the corpses of the fallen mages to become a Harvester flesh golem.
Dwarf Fortress, being Dwarf Fortress, features this. The most prominent example would be the Kitten Rot, one of the many possible Forgotten Beast syndrome. As the name implies, it causes the skin of the infected to completely rot off, leaving behind a horrible mass of living miasma. In its most basic form. If your medical staff is skilled enough, the afflicted may actually survive having their entire skin rotted off. Dwarf Fortress players being Dwarf Fortress players, this has been weaponised. Forgotten beast that rots the nervous systems of your dwarves, leaving them completely numb? Well, looks like you've just got a way to make your military immune to pain! (Also, dwarves without eyes are said to make excellent siege operators, since they don't run away from enemies even though they're civilians.)
Disney's Epic Mickey involves Mickey himself having parts of him melt and drip...upward. Plus the ability to use paint thinner to dissolve your enemies and melt NPCs into little puddle people (this isn't a sanctioned part of gameplay, but it's really funny). There are also dismembered cyborg versions of Goofy, Daisy, and Donald.
Eternal Darkness, a game rife with terrifying imagery, has the Bonethieves. Bonethieves are insectoid creatures with scythes for arms that rip into a victim's neck and enter the body, taking it over and killing the person. The body is then used to attack anyone who isn't infected.
In the Fallout series, ghouls are humans that got lethal doses of radiation but weren't lucky enough to die. They look essentially like walking corpses, though they actually mostly okay people. Also, the Supermutants were all once human but were exposed to the Forced Evolutionary Virus. The Big Bad of the first game, The Master, fell into a vat of the stuff as a human. By the time the Vault Dweller meets him, he's a mass of mutated flesh stretched throughout the foundations of his base, merged into his computers, and has absorbed many other living things/people (minds and memories included).
Just look at Harold. In the first game, he looks like an ordinary ghoul. In the second, he has a tree branch growing out of his head. In the third, the tree branch grew into a full-sized tree, trapping Harold inside and shuffling his organs around in its root system.
Most of the ghosts in Fatal Frame fit this trope. Broken Neck from the first game is a particularly memorable example.
The Blinded Ghost. "My eyes! Give me back my eyes!"
In Fate/hollow ataraxia Caren Ortensia's body reacts to the presence of evil spirits by having spikes erupt from her skin.
True Assassin in Fate/stay night enters the world by eating his way out of the fake Assassin. Who is still conscious and chatting with it. There's a little too much detail about said event, plus the implication that however inhuman True Assassin looks later he is much less so when he first shows up. Couple other examples: Shinji being attached to a faulty Grail and becoming a mutant lump of expanding flesh and Shirou's body turning into swords. No, it is not nearly as cool as it sounds, that's why it's on this page. ...Well, okay, it's cool, but it's definitely not a good thing at all and if they had illustrated the final result it would have been rather creepy.
Finally Zouken rebuilds his form each time his old body breaks down by infecting and fleshcrafting some new victim with his worms.
Sakura's Crest Worm, which, throughout the Heaven's Feel route steadily drives her insane.
There's also Rider's Noble Phantasm, Blood Fort Andromeda, which slowly dissolves everyone inside its area of effect into blood. First their skin melts off, followed by the rest of their flesh, and the bodies are merged together while they are still alive until they are finally absorbed completely. People close enough to the origin of the effect will have all their blood instantly vaporized.
Happens to Shirou in a few Bad Ends, such as swords erupting from inside his chest and having all his limbs removed and his remaining body used as a wand by Caster.
Quite a bit in Gears of War, and loads and loads of it in the Expanded Universe. Lambent humans/Locusts, Sires, the Unfortunate Implications of the fact that Locusts came from Sires who came from humans thanks to the Imulsion, the genetic experimenting and horrible mutations, and not to mention the gratuitous Gorn, and so forth, and all of this just scratches the surface of the video games alone.
The Affliction in Guild Wars: Factions, a plague which initially makes those afflicted go mad and attack anybody who themselves is not afflicted, and shortly after rather violently turn into a body horror. The affliction is later revealed to be the work of Shiro Tagachi (a spirit of incredible strength who 200 years prior had killed the Emperor of Cantha, of whom he was the bodyguard) who was abusing the powers granted him in the afterlife, creating the afflicted instead of guiding newly dead souls to the underworld as part of his plan to return to life.
This happens slowly to Varesh Ossa, whose close tie to Abaddon and his minions caused her first to go bald while developing ridges on her forehead. On death, those ridges transformed into extra eyes as she was resurrected as a Margonite.
The bizarre monsters of Gyossait are supposed to be mutated humans - you even get to see a human mutating into a strange giraffe-like creature. And then there's Uzaza, who somehow went from normal a human being to a giant, tentacled Nightmare Face after grafting a goddess's heart into himself.
In the Half-Life series, parasitic creatures called headcrabs latch onto the skulls of humans, taking over their body and causing gross mutations. These include growing elongated claws, a gaping maw in the chest, and rotting. During all of this, the host is still at least partially conscious. If played backwards, the moans of the 'Headcrab Zombies' can clearly be heard to say "Help God Help! Help me!"
In Half-Life 2, this was changed so that headcrab zombies "merely" have slightly pointed fingers and a large hole in their abdominal cavity. This is compenstated by the inclusion of both fast zombies, which are missing all of their skin and sound like a dog being run over by a steam roller, and poision zombies, which are bloated to twice their width and throw black hissing headcrabs at you. That player could also remove the headcrab from the host, revealing that the host's face is locked into a perpetual scream. Thanks, Valve.
The Overwatch soliders fought throughout and the Stalkers seen in the Citadel are what the Combine has planned for humanity, draining them of "unnecessary" organs and fluids and cramming them with electronics. For bonus points, the other Synth units appear to be this same process applied to various alien species, implying the Combine have done this to who knows how many planets.
And to mix things up, there's the Zombine: A Combine soldier taken over by a headcrab. Unlike regular zombies, they are still connected to the Combine network.
Halo: The Flood. An extragalactic virus with a Hive Mind. Infection forms the size of facehuggers can attach themselves to any body, living or dead, and completely take over their nervous system while simultaneously mutating them into tentacled combat forms or bloated carrier forms. And they always swarm you. To make matters worse, the Flood can regrow their entire population if one infection form is left, and they gain all the victim's memories.
In Halo 3, the Flood Infection Forms can jump onto a human, Elite, or Brute, burrow into their chest (or mouth, in the case of the Brutes), and mutate them into a combat form within a few seconds, complete with horrified screaming from the victim (the cries of the Marines are particularly jarring), sensory tentacles popping out from the point of penetration, horrific gray flesh sprouting across the victim's body, seeing the actual head of the victim. Perhaps the most disturbing part is that when an Infection Form jumps on a character, the NPC will grapple with it for a few seconds to give the player the chance to shoot it off. This means that if any allies are infected, it's all your fault.
A Marine in the level "Floodgate" nicely spells it out for you:
Marine: "I...I didn't have a choice...! The L.T...the Sergeant...they were all infected! I could see it crawling...sliding around beneath their skin! (sobs) A-and then they got up...they s-started to talk! Oh, God! Their voices! Oh, God! No, make them stop! I did them a favor...y-yeah, that's it; I helpedthem! (sobs) Maybe...maybe I need to help myself...(breaks out into sobs)"
In Video Game/Iji, we have Beasts. One would assume they are robots or trained animals. The reality, as the enemy encyclopaedia reveals, is much worse. Those things used to be ordinary Komato.
In Indiana Jones and the Fate of Atlantis, the Colossus of Atlantis is introduced as a machine that was used to transform humans into gods; unfortunately, judging by the hideously deformed bones scattered throughout Atlantis, there were several failed attempts before Nur-Ab-Sal got it right. But even in light of this, Klaus Kerner attempted to use the Colossus on himself during the climax, believing that his Aryan genes would make him immune to that sort of thing. Needless to say, he's proven very wrong: after a brief moment of glory, his left eye swells until it's forced shut, then he begins shrinking rapidly until he's transformed into a twisted little minotaur.
inFAMOUS 2 and the Corrupted. Only during one heroic mission do you witness Bertrand causing the mutation of a perfectly normal man into a Corrupted. It is not quick, and you can hear the man's continuous screams of agony.
If you mess up any of the spells in King's Quest III, you end up with some pretty awful deformities that result in death.
King Dedede gets subjected to this courtesy of Dark Matter in Kirbys Dreamland 3 and Kirby 64: The Crystal Shards, where in the second phase of the battles against him, his belly will open up to reveal a projectile-shooting eye or become a toothy mouth that he'll try to chomp on Kirby with.
Rakghouls in Knights of the Old Republic; here's the Wookieepedia article. In their first appearance, they're somewhere between zombies and werewolves; bitten humans have a chance of being infected and transforming if not cured. They shamble on all fours and balance on their hind legs like nonhuman apes, their eyes have been moved to the sides and squeezed shut, their skins are either a shiny off white or a rough red; altogether they're just monstrous. Rakghouls are essentially ravenous animals.
Star Wars: The Old Republic has a return to Taris and several sidequests where evidence points to the rakghouls retaining at least some measure of their previous sentience.
Though the ordinary Infecteds, Hunters, and (for the most part) Witches in Left 4 Dead probably don't experience much body horror, it's pretty Squicky to imagine what it must be like to watch the formation of a Smoker, Boomer, or Tank.
According to the commentary in Left 4 Dead 2 one of the developers had a "nightmare" folder on his computer with reference photos of people with horrible diseases for reference for making infected. These were so bad that not a single one of them was used as reference for the game.
Mass Effect 1 has Husks - organics captured by the Geth are put onto devices that impale them, replaces their organs with cybernetics and they are effectively turned into cyber-zombies. Also, during the final boss fight Saren's corpse is re-animated into an avatar of Sovereign in gruesome detail.
The background of Dr. Saleon, as told by Garrus. People were used as living incubators for clone organs, and if the organs were bad, why, the good doctor would just leave them in there.
It gets worse in Mass Effect 2. After all, you get Abominations, which are Husks that glow red and explode; Scions, which are three humans fused horribly togther; and Praetorians, tanks made from 30 people fused together and powered by dozens of severed human heads. Plus, the Collectors themselves...
When you find a dead Collector on the Collector Ship, EDI determines that the Collectors are Protheans. However, these Protheans show signs of "extensive genetic rewrite," including three missing chromosomes, plus extensive cybernetic modification. If you ask Mordin after the mission if he thinks the Collectors can be saved, he says "No minds, replaced by tech. No digestive tract, replaced by tech. No souls, replaced by tech!"
Then you find out that this is how new Reapers are made.
You get to watch in horrifying detail just what has been happening to every one of those abducted colonists - you find a pod in the Collector base and get to watch either a Horizon colonist named Lilith or your very own yeoman, friend, and (possibly) romantic interest Kelly Chambers meltinto a bloody mass while screaming in agony, and there's nothing you can do to save her.
In the Overlord DLC, the creature known as the Rogue VI turns out to be an autistic mathematical savant was forcibly integrated into the geth neural network by his Mad Scientist brother to see if the geth could be controlled.
And then Mass Effect 3 came out and took the horror of the husks up to eleven. We have Cannibals, batarian husks with human corpses fused on to serve as an Arm Cannon. Marauders, turians transformed into husk squad leaders. Brutes, enormous krogan husks with a turian head stapled on to provide intelligence. Ravagers, rachni with two huge artillery cannons bolted on, and covered in sacs filled with baby rachni husks. Harvesters, giant insects transformed into flying Reaper monsters. And the dreaded Banshees, asari with latent Ardat-Yakshi genes, twisted and stretched out into wispy monstrosities.
On Mars, Shepard takes off a Cerberus assault trooper's helmet, only to find out he's been implanted with Reaper tech and looks more husk than human.
There's also what's happened to the Illusive Man in your final confrontation with him. He's been so implanted up with Reaper tech that ugly black veins have started growing on his face and neck.
The Harvesters/Ithkul from Master of Orion 3 behave similarly to the Zerg, infecting other races and...reconfiguring...their bodies into freakish shapes. Here (most of the way down the page) you can see some Ithkul - two infected humans, and what appears to be an infected Meklar (yes, they can infect robots too)!
In Mega Man Zero 4, the genocidal Big Bad Dr. Weil is revealed to have his mind trapped in a self-regenerating mechanical suit of armor, which, in theory, makes him "immortal". When The Dragon, Craft, rebels, destroying Weil's base of operations with the Ragnarok satellite, apparently taking care of Weil. That is, until the end of the game, where we see Weil actually survived, and his regenerative armor decaying but still functioning, showing robotic parts meshed with his flesh. Not something to be shown to kids. And then there's his One-Winged Angel, where his armor, but not himself, grows to enormous size. It's obviously a Painful Transformation, as Weil screams during the whole phase, and all the blood.
The X Parasites in Metroid Fusion take over sapient beings, consume their bodies and then mimic their DNA, becoming perfect physical copies and gaining their intelligence...but without any of their higher emotions, living only to feed and reproduce. The Metroids were created to hunt and destroy them, confining them to SR-388, but Samus was hired to exterminate the Metroids. Oops!
In the other two Prime games, there is also Body Horror in the mutations caused by said Corruption, and Enemy Scans of some dead creatures (mutants in the first, victims of the Ing in Prime 2: Echoes).
Mother 3 has the various Chimeras. They range from standard, somewhat silly Mix-and-Match Critters to some...very disturbing combinations. The colorful, cartoony graphics don't help.
Master Porky is at least one thousand years old, and has not aged well. He literally looks like a bloated, pale corpse.
Nexus Clash is a world that contains both plague zombies and necromantic zombies. Thanks to Good Bad Bugs, it's possible for a person's corpse to get ripped in half, with each half reanimated as a different kind of zombie. Which are then forced to fight each other. Thankfully, you don't have to actually watch this happen, but the game describes it to you vividly enough.
OFF: Elsens, who usually look like men in business suits, undergo some nasty transformations when they get pissed off/go crazy and thus become Burnt. Their heads exploding into a fountain of what seems to be blood is the least of their problems.
Pandora's Tower: Go ahead. Try putting off giving Elena the cure for her curse 'till the last minute. You will never sleep again.
In Persona 3, the main character's first Persona summoning. When he pulls the trigger on the Evoker to summon his Persona, he has a really creepy smile on his face, complete with glowing eyes. To top it off, shortly after summoning his Persona, it gets ripped apart from the inside by another, far more brutal and powerful Persona, all while the main character is screaming and clutching his head. Turns out later in the game that the Persona that clawed its way out of Orpheus is Thanatos, aka Death, who was sealed inside the main character ten years prior by Aigis. Considering that the main character's first Persona summoning is against one of the 12 major Shadows used to form the Appriser when destroyed, which also includes Death, this makes a lot of sense.
For being such a light-hearted game otherwise, there's a particularly jarring example in Pikmin 2. "Bulbmin" can be found in certain dungeons, and at first appear to be nothing more than dwarf Bulborbs with a single leaf growing out of their back. Then you look up their entry in the Piklopedia after completing the dungeon and discover that the actual Bulbmin is the leaf itself, a parasitic life form that grafts itself into the bulborb's nervous system through its spinal cord, and controls its actions while the host is still living and conscious.
At first glance, the Pokémon franchise doesn't seem to fit this trope since most evolutions occur in the span of 30 seconds, until you realize how drastic the changes of those evolutions are in only the span of 30 seconds, it starts becoming more terrifying. To put it simply, many evolutions involve the sudden introduction of new elemental types, suddenly growing and swelling to sometimes over double the Pokémon's original size, and many evolutions from originally cute creatures suddenly alter their personality into being aggressive and sometimes even disastrously violent.
One particularly horrific example is Munchlax's evolution into Snorlax. Munchlax starts as a cute little Pokémon at 2 feet tall and a husky 231.5lbs and in the span of 30 seconds balloons into a beast that is three times as tall, and over four times as heavy at a half ton in weight!
Parasect. An animal being eaten inside out and mind controlled by a parasitic fungus.
Seismitoad. A frog that pops the misshapen orbs and bones in its back so hard it quakes the ground.
And then in the real life department, there's some of the animals that the pokemon are based off of. Once again, Seismitoad.
Dusknoir. Yeah, it's a ghost, but still, it has a second mouth. On its stomach.
Any Pokémon that gains new limbs upon evolving may count. Apart from the aforementioned Dusknoir (who starts off as a floating head, then gains hands, then grows arms), Machamp and Graveler are good examples.
Especially pokemon who form new heads, such as dugtrio which are basically three diglett, Dodrio which have three heads, and the collection of egg-shaped pokemon eggicute forming a single tree with three heads. One has to wonder what it would even be like to share a body with newly grown heads or to merge into one entity.
Portal features an energy field at the end of most test chambers, called the Aperture Science Material Emancipation Grill, which dissolves any unauthorized material that's carried through it. While this does not include you and your portal device, GLaDOS is careful to mention that, "on semi-rare occasions", the Grill may emancipate "dental fillings, tooth enamel, and teeth". Yowch.
It starts with a Call Back to the first game; when the automated announcer is explaining the purpose of the Emancipation Grill, it mentions that it "may have emancipated the ear tubes inside your head".
It also manages Body Horror with purely synthetic entities. The "Frankenturrets" in Chapter 8 are a sadistic mashup of a Weighted Storage Cube and a pair of turrets, which hop around pathetically like a crippled robotic hermit crab and make noises that somehow manage to convey their horror at their own existence. To make it worse, they are intelligent enough to be fried by a Logic Bomb.
As bad as the synthetic body horrors are, they pale in comparison to the implied ones you hear about from the pre-recorded messages down in Old Aperture. Seriously, if Cave Johnson felt it important enough to put on a recording, nine times out of ten he's describing the result of some Mad Science experiment the test subjects would have just had performed on them, often simply for the sake of science. These things include having their urine turned to coal, their blood turned to gasoline, being irradiated to cause tumors to grow, being teleported without their skin, having their bones dissolved, or being mutated by praying mantis DNA. Science!
The Perpetual Testing Initiative adds even more Body Horror, turned Up to Eleven for the sake of Black Comedy. Notable ones include a sentient cloud that can leech off people's skins and Man-Mantises.
Villains and protagonist alike of Prototype fall into this; the Redlight virus is designed to warp living human flesh into configurations that would be more useful. The protagonist also has the same charming feeding habits as Aptom of Guyver: he absorbs beings into himself, preferably while they're alive, most frequently humans, to heal himself and gain their abilities, their skills, their appearances - and their memories.
The Puella Magi Madoka Magica Portable game has its own share of Body Horror. For instance, when Sayaka throws her soul gem away and it lands in Charlottes barrier, leaving her a corpse. If Madoka and Homura are unsuccessful in finding it, Kyouko gets the job done a little to late..Sayaka later wakes up again while Kyouko is sleeping and wanders of by herself. When she makes it home Kyousuke is waiting for her, wanting to give her the song he made for her, only to be absolutely terrified at the sight of her. Turns out Sayaka's body is partly decomposed. And since she doesn't feel pain she didn't even notice how half her face has fallen off.
Quake IV is positively rife with body horror, from apparently living human chests with computers for heads attached to walls and the Strogg medical facility level, where the player has to watch helplessly - from first-person perspective, no less - as Cpl. Matthew Kane gets a painful-looking injection of steroids, has his legs cut off with a buzzsaw and new cybernetic legs attached as well as a neural implant stabbed into his brain. The fact that you see all of this happen to another prisoner before you (and hear his screams) does not make it any less horrifying, either. Perhaps the most unsettling sight is that of Kane's bloody leg-stumps quivering after his legs have been amputated. The scene (not for the faint of heart) is here if you want to see it.
The Keeper's Journal in the first Resident Evil is a long, detailed description of the transformation of a normal person into a zombie. It runs from the initial outbreak at the Umbrella Arkley Lab, to the Keeper noticing strange sores appearing all over his body, to him scratching off a chunk of rotting flesh from his own arm and finding himself mysteriously hungry.
The titular character in Resident Evil 3: Nemesis, Nemesis, is more or less a heavily modified version of Mr.X from the previous game and undergoes this process severely throughout the latter half of the game.
Don't forget Dr. James Marcus' transformation into queen leech in "Resident Evil 0''.
Resident Evil 4 plays this with Las Plagas ("The Pests" in Spanish), some sort of strange being that takes over the host's body, and submits his will and mind to Saddler's own purposes. As you play the game, you can see how Las Plagas are slowly taking over the bodies of Leon and Ashley.
Resident Evil 5 has Uroboros. Some of the Majini mutate into nastier forms after doing a certain amount of damage to them, similr to popping off the head of a Los Ganados from RE4 ("the cow" or "the herd" in Spanish).
Revelations might just top all of these with a specific mutation caused by the T-Abyss virus; the Scagdead. Not only is the actual mutation very nasty, but the actual progression is worse; the host is never actually killed by the virus and then resurrected, no; they are still alive and conscious for the duration of the infection. And that happens when you're resistant to the virus.
The Chimera from Resistance; they'll happily mutate anyone into becoming one of them, wrap in cocoons and becoming freaks of nature. Daedalus was once a human...
Resistance 3 allows the player to inflict this trope on enemies with the Mutator, a gun that causes its target to sprout explosive pustules.
Scott Pilgrim, or at least the video game adaptation, has an homage to the Akira example on the Anime page. In the boss fight with Todd Ingram, one of his attacks involves jumping to one side of the screen as his arm mutates, then thrusting his arm at you as it turns into a gigantic writhing mass of fangs and tentacles. However, since Todd's power is derived from his veganism, the arm also contains mutated versions of various vegetables. It might make it worse that Todd has a Slasher Smile during the whole attack.
In Scurge: Hive, you play as a Samus-like space-age Action Girl bounty hunter named Jenosa Arma, who must make her way through an infested research facility. The entire game, she's infected with an alien virus that slowly takes over her body (represented as a percentage). You need to keep visiting decontamination centers to get the infection rate back down, but it will never disappear completely. If Jenosa's infection rate reaches 100%, you'll get to watch as she dies, mutates into an alien, gets up, and howls. It's tiny and pixelated, being on the Gameboy Advance, but it's probably the most disturbing and horrifying way to die in the game.
An unintentional example comes from Sonic & All-Stars Racing Transformed. Switching to front view upon being electrocuted by something reveals that the characters' skulls are completely blank (there aren't any eye sockets, nose sockets, or teeth), they have no finger bones, and only three toes per foot. Granted, the characters' skeletons were obviously sloppily designed because the developers figured that they shouldn't waste hundreds to thousands of polygons on something you'll only see for a few frames, but still!
Isamu in Shin Megami Tensei III: Nocturne starts of as being a completely normal fellow, but as he spends time in the Amala Network, the emotions of people who died in the Conception begin to cling to him, taking the form of screaming faces covering his upper body. The fact that he stops wearing his shirt afterwards does not help at all. He keeps his Nice Hat, thought. On the other hand, Chiaki replaces her missing arm with a roiling mass of tentacles roughly hewn in the shape of an arm. The problem is said tentacles are connected to her body all the way to her face. She eventually ditches the arm in favor of a nicer form. Hikawa instead is connected by several organic tubes from the waist down to his god.
From pretty much every game in the franchise, Fusion Errors are kicked in here by dint of Fridge Horror. How else do you call a failedFusion Dance?
Speaking of failed fusions, in Shin Megami Tensei IV in a certain room in Camp Ichigaya in Infernal Tokyo, you see a couple of demons talking to each other and find out that one of them is a failed result of making a Demonoid, resulting in a low tier demon that is irreversible. Also during the endgame, Walter fuses with Lucifer to help the later regain his full powers. In the Neutral and Law paths, during the second part of the fight with him, his left gauntlet breaks off revealing that Walter's body had not completely sublimated into Lucifer, leaving a twitching, fetus like tumor.
Video Game/Shadowman takes place in Deadside, where all souls are sent upon death. It has plentiful examples of body horror.
The enemies demonstrate how a person's soul degrades after death. At best you turn into a moaning pale rendition of Fat Bastard post-lipo suction; at worst you grow an extra head and lose your legs, develop hooks for hands and grow a gas mask fused into your face; etcetera.
The most disturbing level in the game is the Playrooms, where the "playrooms" are dungeons with blood-soaked floors, piles of torn human flesh, and the hook-handed enemies mentioned above. Really made into nightmare fuel by the children's lullaby music that plays during the level.
Huts and bridges are made out of sewn together sheets of human flesh.
You follow the game's five serial killers by using schism traces- special portals leading to the land of the living. A schism trace is a human body crucified, missing its parts from the waist down, and with all internal organs removed. You open the trace by using an item called a retractor, which rips and holds the body's ribcage open. Jack's diary details the traces, and implies that each body is still alive
In Silent Hill 3, Heather turns out to be "pregnant" with a freakish demon which she is supposed to give birth to.
Many of the monsters, especially in 3 and Homecoming, are quite body-horrific, e.g. the Bubble Head Nurses, the Abstract Daddy, the Pendulums, the Siam, and the centipede made of human torsoes.
The scene where the demon is exorcised from Alessa in the good ending of 1.
On the topic of Silent Hill, you also have Doctors, Nurses and Cybil, when you have to fight her in the Amusement Park. All have been taken over by some manner of Puppeteer Parasite, but the former two have hideous fleshy growths on their backs, resembling massive tumors. Oh, and unlike other monsters in the franchise, they are heavily implied to be real people dragged into the Otherworld and repurposed by Alessa, as opposed to apparitions or creations of Silent Hill made whole cloth.
In the Nintendo 64 game Sin and Punishment, the main character Saki is transformed into an enormous, mindless bioweapon looking like something out of Neon Genesis Evangelion. It's apparently caused by a cascade of blood that inexplicably washes over Tokyo. Eventually he regains his human form, somewhat.
Skullgirls has body horror in spades. Where do you even begin...?
Probably the most infamous example from Skullgirls is Double: a seemingly normal nun who literally turns inside out to reveal her true form, a monster who has the appearance of a constantly-shifting mass of flesh and organs.
Then there's Painwheel, a girl who was kidnapped from a normal life and used as a subject in secretive and unethical living weapons experiments. Her blood was replaced with that of a Skullgirl, the game's titular monstrous entities. Her body was implanted with the Gae Bolga parasite, which manifest as spikes that burst through her skin, and the helicopter blade-like Buer Drive was installed in her back. She is constantly aching, and every attack she does causes her to scream in pain.
Next up is Peacock, a demented little cyborg girl who looks like she walked out of a twisted old cartoon. Peacock is a bit more subtle, in part due to the nature of her attacks and the humor of her character, but the body horror is definitely there. See those cartoon eyes? Those are empty sockets. Her arms, legs, and teeth were all ripped out during the same incident, and were replaced with cyborg parts when a kindly scientist rescued her. She now sees through the eyes on her arms, the Argus system, which give her a decidedly creepy appearance.
Miss Fortune is a Cat Girl bandit who swallowed an immortality-granting gem after a heist gone wrong and was cut into pieces by the group she stole it from. The gem kept her alive even still, allowing her to pull herself back together. At first glance she's not too bad if you ignore the fact that the bones at her joints and the tips of her toes are showing, but her fighting style revolves around tearing herself into pieces (her main gimmick even being keeping her head separated to pull off combos) and her combat involves copious amounts of High-Pressure Blood and using her detached body part in bizarre ways, her grab even has her wrap the enemy in a yarn ball made out of her own muscle fiber.
Despite being a comedy series, Space Quest 4 had a terrifying one with the "modified" survivor on Xenon's blighted surface. Wandering in a daze, yellowed skin, clothed in rags, headgear that forces the eyes to never shut, and only able to utter screams. Space Quest 5 also had the effects of the Primordial Soup - victims literally erupting in pus-filled boils and their bodies melting into unrecognizable piles of goo if left untreated.
The Splatterhouse series holds two examples, both using the same character: Jennifer, Rick's girlfriend. In the first game in the series, Jennifer turns into a monster when you least expect it — right after you believe you've saved her. In the third game, Jennifer is infected by a Boreworm, and your performance in the first couple of levels determines whether you save her or whether she becomes another monster you have to kill.
"Rick, I'M DYING!"/"Help...me..."
The Zerg from StarCraft can "infest" a Terran by infecting him or her with some sort of virus. This turns that Terran into this. With the exception of Lieutenant Sarah Kerrigan and a few others, most infested Terran are deemed next to worthless by the Swarm, and as such are simply made explosive. Despite the fact that their lifespan is really short, because they are suicidal bombs, they seem to revel in it. Kerriganmostofall.
In second game it got worse.
In the first game the Zerg Queen could also produce Broodlings, spores that would consume any biological matter (read: living Human or Protoss) before exploding out of their incubator, instantly killing said unit.
In Star Fox Assault, Pigma undergoes a horrific transformation at the hands of the Aparoids, in which he is assimilated into a spacecraft, turning his whole body into a giant, mutilated, vaguely cybernetic (but mostly organic-looking) pig's face, kept safe in a metallic cube which can open and close, hiding or revealing said face. He then later shows up in Command in an alternate, still pretty weird form - but fortunately, it's much less creepy (and easier to defeat).
The true form of Mimi from Super Paper Mario deserves an honorable mention — if she weren't done in a cartoony art-style loosely inspired by NES games, the appearance of a little girl with a bizarrely-warped, upside-down head with spider legs coming out of it, and her now limp and useless body dangling below her in a parody of The Thing would be Grade-A horror itself, and it still manages to be creepy even with that art style.
Her The Exorcist-esque transformation sequence, in which she breaks her own neck (with an audible CRACK), doesn't help much.
Some of the bosses of Survival Crisis Z are this, including a giant zombie covered in mutant maggots and an Infected with spider limbs for a head.
The annelid Hybrids, and anything to do with The Many from System Shock 2. Imagine a mind-contolling alien parasitic worm that assimilates you into its Hive Mind. Now imagine that worm burrowed into your skull and chest, and that the infection can also mutate you into a monster that doesn't even vaguely resemble humanity anymore. Hearing the audio logs of the crew members that fell under the control of The Many, documenting their slow transformation (often without them even realizing what's happening to them) is ne the most terrifying parts of the game.
The Binding of Isaac. Everything, including the protagonist Isaac, and the enemies he fights. The "powerups" in this game are indeed powerups, but they come with a serious price. Burning off one side of his face with toxic chemicals. Injecting himself with dubious substances. Live flies popping out of his body to attack his enemies. Growing giant twisted demon horns and firing a bloody laser beam from your mouth. All this...and Isaac is only about 8 or 9 years old...
There's also the guy who's turning into a Gibdo in Majora's Mask.
Link's first transformation into a wolf in The Legend of Zelda: Twilight Princess, when thrown into the Twilight Realm for his first time, has a theme of the wolf bursting out from inside him.
The Suffering has quite a bit of this, especially as the enemies are all personifications of different methods of execution: The Festers, for example, represent those left to die aboard a beached slave ship, and are constantly being eaten from within by rats. Occasionally, these bloated corpses will open their bellies and let a swarm of live rats pour out to attack anyone in the area.
Mainliners (representing lethal injection) are in constant pain due to all the lethal chemicals in their veins- as if the stunted limbs and syringed eyeballs weren't bad enough.
Thief II: The Metal Age gives us the Servants. The look like cleverly-built humanoid robots and are sold as such to the City's nobility. Underneath the masks and suits are mutilated vagrants, prostitutes, and others deemed as 'scum' by the villains, forced into servitude by their mechanical masks - you can hear them sobbing and whimpering to themselves. Their existence is so horrific that some of them thank you as they die. Related is the necrotic mutox, also called Rust Gas. It reduces any organic material it touches to something resembling rust, and it will grow until it runs out of organic matter to consume. You never actually witness its affects on a living person...but you do hear them...
Thief: Deadly Shadows offers the Hag as its Big Bad. You learn fairly early on there's something acting as a bogeyman in the City, reputedly having murdered people (leaving variously mutilated corpses behind, sometimes only blood stains). Near the end of the game, you encounter the unusual ghost of one victim, a soul with no human appearance (only a bauble of light). When you lay her ghost to rest by restoring her human-shape, you inadvertently unmask the monster: the Hag, an ancient woman who learned to lengthen her own lifespan by murdering people and wear the flayed skins of her victims as disguises. Her real form is now a tumorous mass of faces, hands, teeth and flesh that move independent of her control.
There are also the remains of the former inmates of the orphanage that was also an insane asylum (simultaneously). They're mummified corpses - but when alive, their hands and heads were locked in wire cages to keep them from harming themselves or anyone else. Now that they're dead, the alien consciousness of the institution puppets them in a freakish, twitching parody of their old lives even as they rot.
The 2014 reboot of Thief has the Freaks, once human creatures corrupted by the Primal into grotesque abominations,
Every game in the Trauma Center series has an infection/virus/whatever ripping people's organs, draining them, digging through hearts, creating reproducing tumors that put bunnies in heat to shame, etc.
In TRON 2.0, a User digitized without the necessary safety features or correction algorithims becomes horribly twisted. Thorne is more or less a living computer virus, and the trio of F-Con execs who decide to take matters into their own hands end up fused into a single, three-headed creature of mix and match parts.
In the surreal Russian game The Void, the cast of beautiful, naked and uncensored "sisters" are complemented by the absolutely horrifying, disgusting flesh and metal abomination "brothers". 'Mantid', as one example, is a quadruple amputee who has various rusted metal protrusions sticking out of him haphazardly, two of which he uses to walk around on as giant, twisted stilts. It is far worse then it sounds.
In Valkyrie Profile, a young princess is force-fed a poison called "Ghoul Powder", which transforms her into a demon and causes her to kill three soldiers. The worst part is that when she's killing one of the soldiers mid-transformation, her innocent, conscious mind is still aware. Not for the easily squeamish.
The fleshcrafting Tzimisce vampire clan get their share of creeps in Vampire: The Masquerade – Bloodlines. First, you find a snuff film in which a woman is torn to pieces by what look like demonic heads with arms for legs. Then you find the house where it was filmed, only to find out the thing is wall-papered in flesh. Then you go into the basement, where you fight the Tzimisce responsible, who summons more of the head things and turns into blood. Then, you have to fight your way through the sewers, where an even worse Tzimisce experiment awaits — giant spider-like things made from the torsos of three women.
Not mentioning Ming Xiao, the head of the Los Angeles Kuei-Jin, who turns into a huge red blob with tentacles and then proceeds to beat the shit out of you.
In WarCraft, along with everything else the Undead do, one notable example in Warcraft 3, where Necromancers (and Rods of Necromancy) raise two Skeletal Warriors from one body...
Also, the aptly-named Abominations, which are monstrosities made entirely out of random anonymous stitched-together body parts (who, by the way, get consciousnesses of their own), all have gaping holes in their chests, leaving their stomachs hanging wide open for everybody to see. Or, whatever else is in there, at least...
From The Frozen Throne, the Crypt Lord can create, from just about any body, some kind of giant beetle.
The Eldan of WildStar were very, very keen on doing all sorts of horrible things to organisms to advance their own purposes. A prime example would be Metal Maw, the "giant robot-fish thing with the laser" in Deradune.
In the in game cinematic for World of Warcraft the Wrathgate, a glimpse of what the plague does is seen as an NPC is briefly seen on his knees clutching his head through his helmet because his face is melting.
The Curse of Flesh is this from the perspective of everyone not already afflicted with it. Trustworthy, enduring metal being replaced with easily corruptible flesh by the will of an Eldritch Abomination, an ever-dying, malfunctioning travesty of one's intended self. The horror tends to be lost on players, since it already turned them into, among others, humans.
The Curse can be reversed, at least for limited numbers of people. They remember their former lives afterwards.
Also from World of Warcraft, the Worgen transformation sequence may constitute Body Horror for some players (the character, starting as human, stares in apparent horror as his limbs turn wolflike, then screams and holds his head as the rest of him transforms).
The raid boss Razorscale may be considered this, although unless you did several quests in The Storm Peaks it may be lost on you. The Proto-Dragon Veranus was captured by Loken. Then Loken fused metal plates completely across her body and, judging from her model, completely replaced several parts of her body to create a "Plated Dragon".
Similar to Razorscale, Deathwing has been artificially covered with metal plates while in hiding. In this case, however, it's to prevent his molten lava interior from just spraying out everywhere.
Once you finally face him in battle, it quickly becomes clear the Deathwing is in no real way a dragon any longer. He's become a Dragonoid Abomination.
The Forsaken. We're talking about, essentially, intelligent zombies with free will. Since they are zombies, they can eat (certain types of) fallen enemies.
Background lore reveals that Forsaken who utilize the Light extensively start to regain some of their lost senses. Some are driven to suicide because this results in them smelling their own rot, tasting their decaying flesh, and feeling the maggots in their body.
X-Com: UFO Defense had the infamous Chrysalids, insect-like humanoid aliens who could turn any X-Com soldier or civilian into a bulging, misshapen zombie with a single egg-injecting melee attack. The zombies are essentially still-living meat-suits for the juvenile Chrysalids, who erupt out of the zombies like someone popping out of a too-small shirt after the zombie takes too much damage.
X-Com: Terror from the Deep had the Tentaculats, who did essentially the same thing.
The things the Aliens are implied to visit upon captured humans. The lucky ones are turned into alien food or dissected, while the unlucky ones...well, the Bio-Drone from Terror from the Deep is a brain in a vat with an anti-gravity base and a sonic weapon, controlled by implanted alien electronics. TftD also features a creature called the "Deep One", which is essentially a living human-turned-alien-incubator. The description of a device called alien implanter reads: "...this [removal/addition of organs and electronics] was thought to be done to unconscious subjects, but research suggests that the subject is conscious and painfully aware. The human physiology fits this device unfortunately well."
The Bio-Drone's sonic weapon was built out of the original human's vocal chords. It screams its victims to death.
Some of the critters from the UFO After Blank series look equally unpleasant, like Cudgels and Dangleflies. Car Crabs, on the other hand, are awesome.
In Xenonauts, the game over screen tells you that what humans survived the alien attacks were modified into unrecognisable forms.
In Yume Nikki, Madotsuki can stumble upon a little girl named Monoko wandering in a tunnel in the White Desert. Seems relatively normal, right? If Madotsuki flashes the Stoplight ability at her, however, Monoko instantly turns into a five-armed freak of nature (one of those arms is coming out of her head!) with what appears to be a melting eye and some sort of vortex in her stomach.
On a related note, the texture maps for almost every 3D character are pretty grotesque when taken out of context. They're sort of...flattened out pieces of people, all stretched.
Kerbal Space Program: This is what befalls the poor unfortunate kerbals who fall victim to the kraken: their limbs flail, distort and stretch way beyond what they should, looking more like what'd happen if you tied a bunch of ropes to a faulty propeller than a humanoid.
Part Time Job has Lyra becoming a severed head in a jar, Twilight and Screw Loose being sewn together and given Lyra's body to boot, and Pinkie Pie getting her hind legs replaced with giant alligator legs. This isn't really anything outstanding compared to other examples on this page, but what makes it even more horrifying is that Fluttershy did this to make them "more interesting" so she could sell them to a circus.
Final Fantasy VII has the boss fight against Hojo: You first fight him as a human, but after you beat him, he turns into Helletic Hojo, a freaking hideous, writhing mass of flesh that wouldn't look out of place in Resident Evil.
The backstory involving Jenova has quite a bit as well. As it's weapon of choice was a virus which drives humans insane before turning them into monsters.
The House Of The Dead Overkill Many of the enemies, especially Nigel and Sebastian (two twins horribly fused together) and the Lobber from Overkill. And from the same game, Varla Guns, after Warden Darling put his mother's brain in her head... and apparently forgot to reattach the back of her cranium. Extended Cut adds the Dual Boss Sindy & Coco, respectively a Distaff Counterpart to the above Lobber in the looks department and a mutant monkey stripper.
Riskof Rain Has this in droves. It's heavilly implied that the player character is doing this to himself just to survive. For instance, Imagine killing a giant magma worm. Upon inspection, it turns out it's eyes are symbiotic creatures. providing the creature sight and the worm provides protection. The player character, in his Sanity Slippage decides to rip out his own eye and replace it with these. Infact, it gets to a point where your character is deemed no-longer human, and in the case of the robot, it merging with the flesh with its robotic hull as a skeleton. Not to mention the engineer who is implied to have merged with the ship itself. The only one that is not subject to this is the Acrid, but they were already a test subject.