The X-Men comics in general feature many cases of Body Horror. For every two mutants, one of the two is deformed in some shape or form due to their powers. Making things worse was the notion of when these deformities manifest themselves; while some mutants are born deformed, others are born normal-looking until they reach their teenage years, at which point their mutant powers kick in and they find their bodies warping, turning them from being handsome/beautiful to being hideously disfigured freaks. Even then, it's a crapshoot towards the extent of one's body horror: Angel and Wolverine, for instance, only suffered minor deformities, whereas mutants like Marrow (bones growing out of her body, which had to be broken off at regular intervals like one might cut one's hair), Husk (ability to develop and shed layers of skin of various biological compositions), or Mercury (body turning into a liquid metal substance) manifest far more grotesque variations. This led to Chris Claremont conceiving "The Morlocks": an underground community of homeless mutants, most of which were mutants that were too deformed to fit in with normal society.
Yet another example would be a nameless and hideous mutant who was shot down by the police before he could "transform" into his "final" form, one which was implied to be of incredible beauty and power. Oh and he was a child too. Crying shame, heavy emphasis on crying.
This is how the evil alien Brood reproduce. They were pretty obviously, ah, inspired by Alien. Oddly enough, the Brood had a Hive Mindfirst.
Masque. A disfigured flesh-warping mutant who got his kicks warping the flesh of anyone who had the misfortune of coming into contact with him? When he took over the Morlocks, following the Mutant Massacre, Masque forced the surviving Morlocks to be his playthings, changing their faces and bodies into such horrific abominations, that the bulk of the community were driven irreversibly insane. Part of this motive was based upon the fact that Masque (originally) was immune to his own powers, which drove him mad because he could alter anyone's face except his own disfigured face. Thought killed off in the early 1990s, Masque returned in Xtreme X-Men #36-39, where he was given upgraded powers: he could now use his powers on himself, which he used to render himself genderless as far as showing the ability to warp his own flesh to go from male to female. However, he was still insane in the head and then some: he used his powers to turn Callisto (ex-Morlock leader who Masque hated) into a tentacle-limbed freak and (with help from his fellow Morlocks) assaulted a subway train full of innocent people and used his powers to disfigure each and every person on said train as an act of mutant terrorism.
Chamber is another X-Man with quite a unique form of mutation; he has a psychic furnace where everything between his upper jaw and diaphragm would normally be. That's no lungs, ribcage, digestive system, etc. Granted, eventually he gets better, but when he loses his power to contain the energy, boom- everything south of his jaw is quite graphically vaporised. He still lives!
Kenji Uedo, full stop. Think of what happened to Tetsuo at the end of AKIRA, now give him full control over it◊. Yeah. Due to his technopathic abilities, he can also force other machines to shapeshift as well, send one way messages through screens similar to Hermit Purple, and let him survive extreme damage due to him lacking organs.
Spider-Man himself. All the mutations he's undergone, from gaining more arms, to transforming into a giant spider (with a description of his feelings in the process) and what happened to him when he was killed.
The Chester Brown underground comic Yummy Fur has such delights as the author eating his own snot (which he has admitted to doing), a man's hand spontaneously falling off, Ed the Happy Clown's penis growing a miniature talking, thinking Ronald Reagan head at its tip, a man who shits so much that he suffocates himself and many others, graphic scenes of penis surgery and so much more. Chester Brown himself, by all accounts has a very amiable, mild personality.
In the two-parter Ruins, Warren Ellis writes about a Marvel Universe where everything goes wrong. Gamma radiation turns Bruce Banner into a green pile of tumors, Peter Parker develops a deadly viral rash from his spider bite, Wolverine is allergic to adamantium, and Johnny Storm incinerates himself.
Warren Ellis seems to love this. Remember Extremis? The cyborg virus that enters the brain? And then causes the immune system to reinterpret the entire body as an open wound? And then rebuild it, resulting in a cocoon of scab tissue?
In Grant Morrison's first story arc for Animal Man, the super-powered (and temporarily insane) Nature Hero B'wana Beast, in a series of failed attempts to rescue his kidnapped ape friend Djuba, uses his telekinetic helmet to fuse various animals together (including a homeless man and a rat). When Djuba dies from laboratory smallpox inoculation, B'wana Beast avenges her by fusing her body with that of Dr. Myers, the scientist responsible. The lab technicians, not recognizing their supervisor, prepare to do ape surgery without anesthesia while their fully aware victim, attempting to stop them, can only grunt "Ma urrs! Ma urrs!"
In Marvel's District X, the mutant Gregor Smerdyakov can't sit anywhere for too long because his feet grow roots that break through his shoes and lash him to the ground. After being cut away from the pavement in an early issue, he later grows into the wall of a sewer channel and essentially becomes an underground tree.
In Marvel's Mutopia X, Agent Popova (after a failed assassination attempt on Daniel Kaufman) was blackmailed into performing favors for Kaufman by having her surgically altered into what many might consider a hideous (or beautiful) mutant appearance.
Charles Burns' Black Hole. The entire graphic novel centers around teenagers who are tragically mutated and disfigured by a fictional sexually-transmitted disease.
Played for laughs in several SimpsonsTreehouse of Horror comics. Most notable example is "Sideshow Blob", where criminal Sideshow Bob (who has a bad cold) is injected with the wrong vaccine by Dr Nick Rivera and turns into a rampaging blob monster.
Swarm the Nazi-Made-Of-Bees was a Nazi scientist studying bees who exposed them to radiation, only for them to mutate and devour him down to his bones. These bees apparently had a Hive Mind, which he became, and lived on as a man made of bees, sometimes wrapped around his human skeleton, sometimes not. This has never really been explored, perhaps because of the absurdity of a colony of telepathic bees with Nazi sympathies, but being devoured and becoming a colony of bees sounds like it would be pretty damn traumatic.
Venom eventually ate the skeleton, but because you can't keep a good Bee-Nazi down, Swarm can now create new bodies by possessing a queen bee and using her hive. He's gone from horrific to pure Paranoia Fuel, a rather impressive feat for a fairly lame villain.
Swamp Thing. Though later retconned into "a plant who thought it was Alec Holland" (surprisingly similar to the Nazi Bee Swarm thanks to a certain infamous memory experiment involving flatworms that wasn't debunked till much later) the original story was a man turning into a strange plant monster, incapable of even speech, and having to try and cope with it.
Later on, around Brightest Day and the New 52 reboot, Alec was brought back from the dead, and it turned out that the plant that thought it was Alec was an accident - Alec himself was supposed to have become Swamp Thing. And since Alec was back and the plant was out of the picture, Alec found himself targeted for the transformation.
His Marvel (sort of) equivalent Man-Thing is potentially even worse. There is virtually nothing left of Ted Sallis's mind in Man-Thing; Man-Thing doesn't need to cope, because most of the time, he's not even sapient. The fact that all those who know fear are horrifically burned more than makes up for that in terms of Body Horror.
Stone Island. Harry's transformation into one of the creatures, which starts with him puking his guts out and doesn't stop until he's a seven-foot-tall monstrosity with no eyelids, a permanent grin in a distorted face, and hideously lengthened skull.
The second issue features a man who has been engineered into a killing machine. His body is half gone. His cock has been connected with the parts of his brain that spark up when he kills things. He's still sentient... but just barely.
In the ninth issue, a Frequency agent investigates a medical facility dealing in top-of-the-line stem cell research that's cut off all communications to the outside world. Turns out the doctors went insane from the gas leak and decided to build a temple to the wonder of the human body. Using all the patients as bricks, and the stem cell technology as mortar. And they're all still alive.
In DC Comics, one Superman issue saw him fly to the edge of Creation fighting Darkseid and, lo, they beheld... an infinitely vast wall of living, breathing, screaming flesh and faces that act as the "wall" between Creation and the nothingness beyond, the Source Wall. Its current form is apparently made of everyone who's ever tried and failed to pass through it and discover the secrets hidden on its other side.
Oftentimes characters who are effectively immortal or have "healing factors" will venture into this territory. The Ultimate X-Men version of Wolverine has been subjected to such horrors as regrowing his entire body after being decapitated and having the flesh stripped entirely off his bones but still being alive. Orson Scott Card's "Ultimate Iron Man" gives Tony Stark similar powers (for some reason) and has many creepy scenes of him regrowing his various severed limbs (which he loses so often, it becomes a running joke). In a particularly strange example, The Savage Dragon had the mood spoiled during sex when he and his girlfriend are horrified by the sight of his severed arm suddenly and unexpectedly regenerating in a gruesome fashion.
Hulkling of the Young Avengers was once vivisected. And guess what? His organs move while he's unconscious to protect themselves.
Then there was the time Hulkling was captured by the cosmic parasite Mother. The next time we see Mother, she's sitting on a bizarre chair made of frozen green tentacles. Then you notice the chair has Hulkling's face...
There is an 80s issue of Captain America vs Batroc, where the U.S. Agent side-story in the latter part featured a guy who appeared to be undergoing extreme steroid enhancement(to the point that he was paralyzed due to his muscles expanding too much to allow movement).
Explored in "What If The Fantastic Four All Had The Power Of The Thing?"
Reed Richards' stretching can cause mild body horror sometimes. Especially if you think about what stretching like that would feel like. Reed doesn't seem to mind. He thinks it's useful.
Something like this happened to Johnny Storm while he was held captive by Annihilus. He is repeatedly killed, only to be brought back to life, often times stitched back by worms... it's not very lovely.
A particularly chilling example from Captain Britain: a fellow named Sid managed to survive an encounter with the omnicidal Attack Animal known as the Fury, getting away with only a scratch. Unfortunately, the Fury's scratch was infectious, and the results were not pretty. Not by a long shot.
Widespread in the nuclear war wastelands (known as the "cursed Earth") with rampant radiation-induced deformities.
It is common in Judge Dredd's Mega City-One where people willingly inflict body horrors on themselves such as The League of Fatties, whose sporting events include extreme eating and fat contests (the fattest person wins 50,000 creds and tons of endorsement deals).
Explored in Judge Dredd (reprinted in Complete Case Files volume 4): "ugliness products", i.e. skin mold cream, tooth decay gel, dead skunk aftershave, etc., that are popular in a society in which any nonmutated human could achieve beauty.
There are two Judge Dredd stories dealing with humans being mutated into a giant spider. One is told in a tragic manner concerning a woman. The other is told in a comedic manner with the victim being a man.
There is Deadpool, whose skin appears to be horrifically burned or surgically removed. At least he has a holographic projector to alter his appearance. It's cancer. All of it. He had a healing factor installed in an attempt to cure his cancer, only to have the cancer become his healing factor. Dude is a walking tumor.
While fans hated him mostly for his completely different character, the Ultimate Marvel version of Deadpool isn't any better; his face is gone, leaving his head a naked skull, with eyeballs and an exposed brain, wrapped in translucent plastic.
The Warhol virus from Wildstorm: World's End is named so because it keeps the victim alive for about 15 minutes while the victim is turned into a hulking, disfigured maniac.
In Warren Ellis' writing of Stormwatch, the Island of Gamora launched a watered-down superhuman mutagen upon an English town. Most victims were rendered as horiffically mutated corpses. The unfortunate surivors were fused into a giant mass of flesh whose hands were fused together in a shape similar to that tubular seaform known as a lamprey.
Similar is the Basilik's cult cyber-zombie virus from Suicide Squad (the New 52, volume 4). One unfortunately cursed woman was turned into a giant, tentacled blob and thankfully killed (as she requested).
Ultimate Universe Red Skull: not liking the fact that he looked like his father (Captain America), the Red Skull removed his entire face and scalp.
Rat-Man combines this with Gory Discretion Shot. Evil Albino Janus Valker gets hold of a device that allows travel in parallel dimensions, but that one is malfunctioning and manages to materialize every other Valker in existence simultaneously inside the body of the first one. We only get to see an arm erupting from Valker's own arm before cutting to Rat-Man and his friends witnessing it. Their horrified faces and the narration are more than enough.
Rhona Burchill augmented her intelligence by literally placing some of her brother's brain matter in her own brain, causing her head to become hideously disfigured in the process.
In Enigma, several comic book villains come to life... as more horrifying, mutated versions of their more light-hearted comic forms. And each of them starts out as a normal human. Granted, they're not all terrible, but the first guy got it pretty bad. And then there's the Enigma's own mother, who does this to herself in a fit of apparent insanity, and takes it up to eleven.
In King City, users of the drug "chalk" eventually turn into more chalk. In both cases we see on-page, it starts with the hands. This is what eventually does Max's old war buddy Tooth in; by the time Max gets there, the hazmat crew/drug dealers are hauling him off and all that's left is a Chalk Outline.
The New 52 rendition of The Joker has a fellow villain slice all of the flesh off his face... then the Joker reattaches the skin to his face with straps sewn into the skin.
In The Trial of the Flash, Big Sir mutilates Flash's face with an energy mace, distorting it beyond recognition. When a couple of kids unmask the Flash, they scream in terror and run away.
In Transformers: Generation 2, the Cybertronian Empire boosts its population via Budding, a long-hidden method of Cybertronian reproduction. We see what the process entails at one point: The surface of the "budder" practically comes alive, and slowly forms into a living mechanical foetus, which tears itself free of the host body. While this is happening, the first mechanoid is writhing in pain and discharging all kinds of energy.
Some of Batman's Rogues Gallery have this as their schtick, most notably Clayface III, who must stay in a containment suit because his touch disintegrates any living thing he touches, and The Corrosive Man, whose skin releases acid and he can feel every bit of it.
Transformers: More than Meets the Eye introduces Empurata, a technique employed by the old and corrupt Senate. Basically, they have the head and hands of the victim removed and replaced with boxy cycloptic heads and claws or clamps for the hands. A few of the big named characters suffered this, notably Whirl and Shockwave.
The Post-Crisis Superman story that introduced Hank "Cyborg" Henshaw, which is basically a riff on Marvel's Fantastic Four, is loaded with this. Four NASA shuttle crew members encounter a type of radiation and suffer bodily mutations. One of them, as an example, has his body reformed into a mass of rock (a la the Thing) only with pieces of the shuttle mixed in. The pain drives him to commit suicide by way of an MRI machine, which rips him apart.
The original Omega Men series had Kalista get mind-raped by an organism which did so by stealing her shape and memories, leaving her an unrecognisable blob. While this is happening, she starts losing her shape, then her features, then her ability to perceive things, then the ability to think. It's horrifying, and it doesn't help that she begs for it to stop the entire time.
2000 AD: The premise of The Visible Man is of an ex-soldier who gains partial Invisibility from a freak accident involving nuclear waste so that all his internal organs are showing. People shriek in terror at the mere sight of him.