Whomp!: This comic (25/4/2012) deals with what happens when your flesh falls off. Urgh.
In Stand Still, Stay Silent the way Rash victim's bodies transformed into trolls is... squicky. Especially after you realize that trolls and giants are made of people and suddenly you see body parts all over them...
Gnoph has a lot of this. When it begins, Abbey is being slowly eaten alive from the inside by her Bond Creature, Scut. Things get progressively worse from there.
In the Order of the Stick prequel volume Start Of Darkness, Xykon rips away his own flesh as he is transformed into a lich.
8-Bit Theater has Red Mage getting raped by and transforming into what can only be described as a "hideous eye thing" and later having partial transformations as he tries to bend the laws of magic in order to hide the fact that he was still a monster.
Vladia, (formerly Vlad) from El Goonish Shive is a shape shifter whose form was a mishmash of bats, birds, human, an alien race known as Uryuoms, and a freaking leopard, wouldn't change out of his/her animal form due it being excruciatingly painful, and potentially fatal to take on his/her human appearance. Even though we don't see the Body Horror, it's very much implied, considering the above and that this is her as a human◊ and is her animal form◊.
In Homestuck, when each character enters the game the antagonists are "prototyped" with a new mutation. When Jack Noir kills the Black Queen and takes her magic ring, he loses an eye and an arm, grows a jester's hat, a cat face, tentacles, and wings, and then grows a sword through his chest. And that's just with three players in the game, there's still one more to come!
Jade's Kernel ended up being prototyped with Bec through a series of unfortunate events. We get to watch Jack transform into an almighty godlike being with unfathomable cosmic power.
For more prototyping goodness, there's the prototyping of Jane's sprite with Vriska and Tavros's corpses, resulting in a being that knows just how horrifically wrong it is, both physically and mentally. So much that Tavrisprite blows itself up a couple pages later.
This is also played straight with Erisolsprite, the combination of two trolls that nearly killed each other when they were alive. They're just stable enough to not share Tavrissprite's fate, but they're still in a constant state of self-loathing. However, Dirk's sprite averts it completely. Lil' Hal loves having a physical body, and Equius loves having a powerful robot brain. There's also Roxy's, who has so far been the speechless but seems to be quite fine with the combination of Nepeta and Feferi - justified in that the two components were the friendliest and most peaceful of their peers. Then Fefeta is literally torn apart from the conflicting emotions during an argument between Erisolsprite and Arquiusprite, playing the trope straight.
In the comic Wurr, the hellhounds have been exposed to mutating Black Touch for generations, resulting in strange mutations such as extra limbs, eyes, too many teeth, strange skeletal structures, and countless other strange features. Some hellhounds, called Whispering Ones don't even have proper genetalia.
In Demon Eater, every time a demon eats another demon, the eater's body changes to take in some characteristics of the eaten demon. Demons can also shapeshift at will, but that has happened less often.
Body horror is a possible random side effect triggered by the Shield of Wonder. Notable cases are the guard who was balefully polymorphed into an ogre and cut down by his sergeant, and one who was painfully transformed into a swarm of snakes.
The finger horror spreads a disease called 'liquid rot' to any living thing it touches. The limbs of creatures affected by this disease will transform painfully, before falling off the body and turning into a liquid goop which the horror can feed upon.
And it won't even try to kill you quickly, either. It'll drag to its lair, infect you with the rot, and leave you to die a slow, agonizing death before feeding on the remains. As deaths by liquid rot go, this (spoilers) was relatively quick and clean. Says something about the setting, no?
In one of the early Looking for Group comics, Richard cast a spell to create skeletons to fight on his side. Said skeletons were still in the bodies of his enemies, which the skeletons hastily extracted themselves from. Did I mention said enemies were still alive?
Mrs. Cho of The Bongcheon-Dong Ghost. Her body is not necessarily strange looking and retains human qualities. It's the fact that she is the reanimated corpse of a mentally unstable woman who committed suicide from jumping from her apartment window that enforces the horror. When Mrs. Cho hit the ground, every bone in her body retained damage of various levels. Some had small fractures but many were split in two. In addition, her forehead most likely hit the pavement but caused no damage to the skull. If that had happened, her head would be destroyed. This injury causes her head to retain its shape while covering it in blood. So to reiterate, she is a walking corpse who broke every bone in her body whose face is covered in blood. The real frightening aspects of the comic are two jump scares when Mrs. Cho turns her head 180 degrees around and runs faster than a cheetah on crack directly at the screen while unsettling noises of bones cracking are heard. Also, Mrs. Cho was a real person who committed suicide.
The Kingfisher features a moderate amount of body horror, especially when new vampires are born, or when a vampire assumes the form of their death.
Played in disturbingly realistic fashion in Sunstone when we're shown the dangers of careless rope work in self bondage. Marion uses the wrong sort of knots on her wrists combined with improper positioning of the ropes on the bed out of obsession with trying to prove Alan wrong about 24/7 submission (which Alan isn't into for a variety of reasons, chiefest among them being that it is highly stressful for the dom), and finds herself trapped and alone while the blood circulation to her hands is cut off. and finds herself trapped and alone while the blood circulation to her hands is cut off. Her hands go lifeless and visibly dark grey in colour. It gets worse when we're told this had caused blood clots and Marion could have lost her hands.
And it gets even worse with the realization that had Ally not known to keep the ropes on her despite Marion's desperate pleas to take them off, Marion could very well have died — if those clots had been allowed to run loose in the rest of her bloodstream, the most probable result would have been a heart attack or a brain embolism, depending on which major organ the clots got to first.
False Positive played this painfully straight in its very first story arc.
In Pacificators, this is Nozomi's preferred method of attacks. She uses her powers to do things such as: tearing a man's heart in half, sucking the air out of another man's lungs, and her special favorite, bursting a man's testicles.
GuildedAge has The Grove of Ur-Animals, which contains monsters that even the In Harmony with Nature wood elves won't go near. The nicest-looking is a giant gorilla, with eight arms arranged like spider legs and eyes to match.
Coga Nito: Potentially with Pieces. The user's body physically turns into the Piece, along with anything they're wearing and any objects they're holding. They can also potentially take horrendous damage, as long as the head is unharmed.
Baskets of Guts has some really gruesome scenes. Especially those involving magic.
Zarla'sUndertale comic about an alternate universe where Sans and Papyrus become an amalgamate is quite horrifying. The way Sans' and Papyrus' body's melt together is just as horrifying and saddening as the canon amalgamates.
A constant in Awful Hospital, especially once you see the world beyond the Polyp.
It's later revealed that the Hospital is so alien that the very idea of a human is fundamentally incompatible with it, leading to theirtransformation into the creatures that Jay refers to as 'Slobs'◊. According to DoctorMan, Jaynote pictured in both of the linked transformation sequences is even of exceptional stability among humans 'admitted' to the Hospital.
Mare Internum: First, Mike gets a compound fracture to his femur. Then said femur gets some weird parasitic growth that appears to have a mind of its own. Now there's something on Mike's face... something that seems to be living, and stuck.
Avialae starts with Ordinary High-School Student Gannet finding out that he's suddenly begun growing wings from his back. It does NOT make for a pretty picture with copious bleeding and intense pain for him. This is thankfully limited to just the early stages, though; his wings keep growing, but they stop bleeding after the first day of growth unless they're improperly bound.