Gantz had this since the nearly the beginning, but aliens seem to be getting worse as the manga goes on, especially in the second and third parts.
The Nurarihyon alien starts out looking like a small old man with elongated ear lobes, then he's attacked and mutates into: A girl that grows into a woman in seconds, a giant, an amputated, laser firing giant head that later grows legs, a tall woman, 4 tiny old men, a golem made of human bodies that dissolves the body of a rapist Gantzer, a deer-headed beast, a mixture of the previous, a mimic of Oka's Gantz Suit, Samara Morgan and a demon-like, skinless creature full of spikes; plus, the last few forms he assumes after being mostly destroyed, regenerating in a very graphic manner from detailed piles of flesh, blood and organs.
Monsters in Katastrophe are an embodiment of this trope, some being barely human.
Reika's team ends up fighting a seemingly endless array of monsters that seem to be random amalgamations of human body parts, most of which transform rather grossly. Before a chicken-like being exploded in a room full of refugees, freeing shiny bubbles that cause humans mutate into monsters at an alarming rate. The mutations force vicious heads that look the same as that of the infected person to sprout from bloody holes opened from the inside of the body by hands. It doesn't help that the heads come in various sizes and can swallow or munch a human whole.
Kanon 2006, when Mai shows Yuichi the state of her skin as she slew more and more demons that plagued the school.
It's actually much more horrible than described here, because Tetsuo, while his body is growing horribly, actually crushes his girlfriend inside himself while screaming for somebody to save her. That detail alone can keep you from sleeping for many nights after watching this movie.
Even more horrible, due to his psychic powers being completely out of control, not only was his body crushing her, he was psychically linked with her at the time. So he felt her pain while he was inadvertenly killing her.
The Akira transformation scene is satirized in an episode of Robot Chicken with Mrs Claus turning into a big octopus-like blob monster. Even the Gainax Ending is parodied by Santa shouting "My wife! What the Hell just happened to my wife?!"
In Blood+ the Chiropteran outbreak is the epitome of this trope.
In episode 14 of Thriller Restaurant, Anko's wart takes control of her body and mind. It also manages to swap faces with the real Anko.
In Bleach, Mayuri Kurotsuchi's first introduction has him sever his arm and then regrow it. Thankfully it does end in a normal arm, but the images are disturbing enough to qualify. This was downplayed in the anime.
Mayuri later fights Szayel Aporro Granz, who uses his tentacles to impregnate Mayuri's Opposite-Sex Clone daughter with himself (through her navel), and births himself through her mouth in the anime or rips her stomach open in the manga, leaving her a barely alive husk. Mayuri kills Szayel with a chemical that speeds up perception faster than the body can react, so death feels like it takes an eternity. Then Mayuri rapesdoes something to his daughter's near dead body to bring her back to full health.
The "does something" part is lampshaded by Renji and Uryu immediately afterward in the manga. Surprised, they ask what Mayuri did that immediately restored her life, and in full health. He doesn't answer, leaving the two wondering what he did.
Renji/Uryu: She's fixed! B...but how? How did you fix her with what you just did?
Mayuri: My...so even after seeing you can't understand? What a waste.
Renji/Uryu: The hell I'd understand! All you did was some stuff we weren't able to see!
Mayuri: Hmph...in any case, it's impossible for such mediocre people to understand my arts.
In the Anime, they break the fourth wall, saying that Mayuri did something that they couldn't show the audience. Mayuri responds that the two have their minds in the gutter.
Let's just say everything Mayuri does eventually devolves into this trope.
The anime, in turn, has a scene in the second episode where Orihime's dead brother Sora gets eaten and transformed into a Hollow. Which didn't happen in the manga.
Similarly, Numb Chandelier mixes this with People Puppets as she shoots her seeds into the bodies of Tatsuki, Chizuru, and other Karakura students. When we see Tatsuki and Chizuru up close, the veins in their bodies are horribly dilated and almost see-through, and both girls are forced to beat up Orihime despite their struggle.
The effect of the Barragan Luisenbarn's power: age. Unreleased, merely touching him can weaken bones enough to make them snap like a twig. When he releases, well...his attack ages the flesh right off your bones and keeps spreading.
Kubo has once again surpassed himself in terms of nightmarish images: Tousen's Ressureccíon has him, a perfectly human-looking rogue shinigami, not some hollow, arrancar or anything else you would expect to pull some monstrous One-Winged Angel on you, turn into a big, hunched, furry insect monster with four arms, insect wings and big horns on its back. Doesn't sound any scarier than your average monster of the week? Well, that's because I haven't mentioned the face yet. In this form, he has a head twice as large as a human's, with no nose and two bulbous eyes which look like a piece was cut out when he opens them to reveal his pure black, oval pupils. And the worst is: his mouth and chin still look human!
Aizen transforms progressively into stranger forms with the hougyouku, but the last form more than qualifies for this trope. His face tears open to reveal a blackened skull with a third eye in the forehead, the remains of his face hanging from the sides of the skull. His body is white with 3 holes in his torso and he resembles a regular Hollow more than a human being. 6 malformed, eyeless vaguely humanoid bodies and thick tentacles grow from his back, and his right arm is replaced with a long thin blade which is actually his own Zanpakutou fused to his body. Given he claimed he would never turn himself into an Vizard yet clearly resembled a Hollow at that point, he might not have even been aware of his own transformation.
The anime extended the transformation, starting with the jewel on his forehead exploding violently into the third eye and bleeding. It more than likely caused some severe head trauma or even brain damage considering what happens next; his neck actually snaps with an audible crack and his face even folds before his eyes abruptly focus. While the face-splitting isn't shown, the energy pillar generated from the transformation actually explodes from an excess amount of blood just after the wings violently shooting out of his back.
Captain Unohana's bankai - a blade of blood that melts the flesh off people's bones - including hers.
Devilman: Any creature you can find in this series counts, including the main character. Amorphous slimes fulls with eyes, fangs and tentacles and oozing vile fluids are the less nightmarish thing you will find.
Everything by manga artist Junji Ito. He is especially well-known for Uzumaki, a three-volume manga about a town that is "infested by the spiral," which manifests itself in various horrific ways. You will never look at a cinnamon roll the same way again.
His manga Gyo might be a better example, since in Gyo, the characters themselves remain conscious enough to realize what is happening to them. Also a classic example of From Bad to Worse.
Likewise, his manga Tomie is about a girl who can regenerate From a Single Cell. This regularly results in things like her growing extra heads from her wounds, or her severed limbs regrowing bodies of their own.
The manga Franken Fran exists solely for this trope. In an early example, Fran is asked by a cop to look into a rash of severed limbs. She finds they're all from the same person, which seems impossible given there are far more than two arms and two legs in the pile... then she tracks them to the source. It's a young woman whose body has a massive oversupply of stem cells, causing her to continuously grow limbs and organs - she is trapped in a gigantic, ever-growing tumor. Her parents took to hacking off the spare limbs to keep it under control. Oddly enough, that's one of the few chapters with a happy ending.
A similar thing happens in a later chapter to a woman who hires Fran to give her immortality, and Fran does exactly that, converting her into the one type of cell that isn't pre-programmed to die: cancer cells.
This wasn't what Fran intended. It was a potential side effect Fran was attempting to fix, but she tried to kill Fran, then stole and used the treatment before Fran could fix this problem. The series is big on Laser-Guided Karma.
A common aesop to each chapter is why exactly we don't do certain things, like trying to be more anatomically similar to anime characters (you need your skull redesigned and have to use silicon baths to keep your face from falling apart), resurrection (the person who died might not want to be revived), immortality (above) and superpowers (human bodies are not designed to maintain superman-level powers).
The transformation sequences in Xam'd: Lost Memories can be quite gruesome if you're not prepared, including a scene where the protagonist is enveloped by what looks like white paint sprouting from his oversized arm, and ends up turning into this◊. The storyboards for this sequence are even more off-putting.
Strait Jacket is set in an Alternate History where the Industrial Revolution was powered by sorcery; unfortunately, sorcery has some horrifying side effects in the form of the Malediction, which transforms Sorcerists into insane, screaming monstrosities bent on killing everything in sight. Sorcerists can stave off the effects of the Malediction by suiting up in Powered Armor called Molds, but even these aren't foolproof, and using sorcery with a damaged Mold is guaranteed to turn the wielder into a nightmarish demon.
G Gundam has the DG Cells, which completely corrupt your body and your mecha and have a disturbing level of control over your whole self. Almost every single person contaminated with them ends up dying messily. Only Allenby, the Shuffle Alliance and Saette survive. And in the case of the Shuffles, it took an Heroic Sacrifice to de-brainwash them.
Assimilation by the ELS in Gundam 00 Awakening Of The Trailblazer. Consists of your body turning into metal from the inside out, with metallic crystals growing out through your skin as it happens. Everyone it happens to is screaming in pain as they die. Worse, some ELS didn't have enough raw material to fully convert a human, leaving at least one girl only halfway assimilated: half her body human, half metallic spikes. Once the ELS have a better understanding of humans, they refine the process so that it is both nonlethal and voluntary: said girl is shown in the epilogue to still have a half-ELS body, but now shaped fully human and living a normal life.
The various humanoid corpses in Shikabane Hime: Aka also take on rather delicious monster mutations when their true nature is revealed — as seen from the intro, showing a large (and growing) mess of flesh and appendixes.
Gatekeepers eventually reveals that the Invaders the titular characters are actually normal citizens transformed into evil alien clones. Initially, it had not been made clear whether the Invaders took over ordinary people, or the ordinary people had been sleeper Invaders all along. Either way, the transformation was pretty horrifying for someone undergoing it.
Invaders are sleeper agents in the main series and The Virus in 21. This trope is far more in effect in 21.
Mazinger Z: Several of them: The Iron Masks and the Iron Cross are corpses turned into cyborgs, and if you remove their helmets, you can see their brains, with tubes and circuits sticking into and out of the brain matter; Baron Ashura is a half-male, half-female cyborg, since Big Bad Dr. Hell stuck together two halves of two different mummified corpses -and he is a shape-shifter, too; Viscount Pygman has another person sticking out of his neck instead of a head...
Great Mazinger: The Kedora were brains of Mykene soldiers grafted into a... kind of freakish creature (it is a kind of amorphous, dak blob full with jaws, eyes, tendrils and wings) capable of eating metal and fusing with a machine to give the soldier's brain complete control of it (so giving birth a new Mykene Monster Warrior); Hadias, General of the Mykene army of Evil Spirits, is a giant skeleton with an upside-down, flaming skull for head, another head replacing his left hand, another upside-down skull replacing his groin, and his true head sticking out of his chest.
UFO Robo Grendizer: Gandal was a being with split personality. One of his split personalities inhabited a tiny female body was inside Gandal's head. Every time that personality wanted voicing out her opinion, Gandal's face split in two halves bent outwards, and she emerged out.
Neon Genesis Evangelion: When Armisael invades Unit 00 and Rei, and all the clones of Rei, and the impaled body of Lilith complete with many many little legs growing out of it.
Arguably the situation for the human souls attached to the EVAs, indeed bordering on And I Must Scream.
After Gendou implants ADAM in his own hand.
In the manga, Gendo eats Adam.
Hell Girl. In season 3, The Cauldron of Three, Enma Ai has no body. So what does she do whenever she needs one? She grows it out of a giant cocoon that emerges from the back of Mikage, her Demonic Possession victim. Poor Mikage screams every time.
It's supposed to resemble the chrysalis of a butterfly.
Possibly even worse is at the end, when Kikuri temporarily grows a third eye, and then her head falls off and turns into a spider with three functioning eyes on its abdomen. Said spider then crawls out from under someone else's eyelid in the same episode.
Several enemies from Getter Robo, with the most popular being Armageddon's Invaders, a race of Nigh Invulnerable amorphous black blobs covered in eyes and bony protrusions, that make the lovely sound of snapping bones while moving.
The manga Getter Robo Go has Shin Getter Robo absorbing it's pilots, the Big Bad, the Big Bad's fortress, and a good chunk of the north pole to become a moon sized robot before flying off to Mars. The last page of the manga shows a fossilized Shin Getter with Go's face sticking out the side. Later stories reveal that Shin Getter eventually absorbs Mars, becoming the Getter Emperor, out grows our galaxy, and defeats what is alluded to be God.
Unico in the Island of Magic, had a puppet-master villain with bug eyes and the ability to distort his shape at will, as well as plenty of terrifying transformations. The villain's castle is built out of people who have been transformed into blocks and there's a creepy dream sequence where Unico and his friends are turned into dolls.
Vash's Angel Arms transformation from Trigun were horrifying the first time, if for nothing else because he has no control. Vash is screaming his head off in a combination of terror and panicked memory, just trying desperately to get the thing pointed skyward so that he won't do any more damage to the city. It doesn't work.
More specifically: what begins with his revolver spinning a small cylinder of white matter continues with said cylinder apparently morphing with the revolver and the arm, and finishes with his arm splitting down the middle with a glowy Orb of Death thingy suspended in it. Then again, Knives appears to do it casually, so it's conceivable that the process itself is painless - Vash only screams because he is being forced to do it to hurt/kill people against his will.
In Digimon Adventure the Big Bad Myotismon proves to be Not Quite Dead, and to complete his resurrection, his bats devoured his minions for their data and formed a new body for him, a massive and creepy-looking demon. Worse still, when the heroes use their strongest attacks against him they release what he calls his true form: a small, impish creature that emerges from his crotch.
Then there's Skull Greymon, who, according to its official bio, focused so hard on fighting that it fought until its flesh wore away and it was nothing but bones. Imagine what it looked like mid-transformation. Yikes.
And the Rookie-to-Champion digivolution sequences in Tamers, which all involve the Digimon's skin peeling off, their wireframe morphing into that of their new, more powerful form, and then their skin coming back and reattaching itself.
It's somewhat less nightmarish when you consider that their "skin" is actually just a texture map. But still...
With all the transformations going on in Dragon Ball Z, some were bound to be nasty.
Cell's reverse transformation where he vomits up Android 18.
First-time Super Saiyan transformations aren't too pleasant. Goku and Vegeta in particular seem to really suffer.
Majin Buu's ability to pour himself down his victims throats.
If you pay attention, Frieza's transformations weren't exactly comfortable. First his body gets swollen to ridiculous sizes at random intervals, then he has the spikes jutting out of his back and his skull elongating, then finally all of his skin shatters from his body like glass with long audible cracking.
The resurrection of Trisha Elric at the beginning is a Came Back Wrong example of this trope, and would be horror enough for any other series.
In one of the openings, if you look closely, Envy comes out of Gluttony's mouth. And Lust comes out of Envy's mouth.
Envy's true form: Most of his body is made up of human faces. His transformation into his true form at least looks incredibly painful.
The scene in Brotherhood where Lan Fan grabs Greed/Ling's hand when he's about to fall over a cliff. This is in the manga too, except that it doesn't show blood running down her arm from where her automail arm was pulling out of her flesh. Ow.
A sentence that results in pure horror: "What If I were to give birth to humans?" Father gives birth to humans, alright. More accurately, horrible, human-like shells housing the souls of Hohenheim's Xerxes friends, including several of his slave friends, his master and the king. And they are visibly melting by the end.
How about Father battling all the alchemists with Greed's hand literally stuck in his face?
The first anime adds in Tucker accidentally turning himself himself a freakish humanoid chimera in an attempt to revive Nina and the return of Gluttony in the movie.
In Saikano, Chise's transformations into the battle-mode of the Ultimate Weapon cause her to sprout metal wings on her back, which appears to be extremely painful. As the series progresses, her transformations become more and more intrusive and nightmarish — including mentally. In the end she is only human in outer appearance.
The anime doesn't make it seem painful until the second half of the series.
Naruto's later Jinchuriki forms involve his skin ripping away like paper while huge globs blood come out of him, his skin turns to ash, and then red chakra forms a fox-like shape around him. The six-tailed form adds a giant skeleton around him, and the eight-tailed form creates muscle tissue around the skeleton and recreates the fox's face. Now not an issue since Naruto has Nine-Tailed Chakra Mode and Biju Mode.
Sakon and Ukon have the power to merge with the body of anyone they touch, which took the form of having their head stick out of Kiba shoulder like a tumor and mention it can also break off parts of their enemies bodies.
The Kimimaro battle. Anyone who pulls out his own bones to fight is a shoo-in for this trope.
Orochimaru's true form; A white snake with snakes for scales who steals people's bodies
Kabuto takes bits of Orochimaru's DNA and fuses it with his own to find out if he's capable of resisting its growth. It was bad enough in the beginning, but now he even has a snake growing out from his stomach. And now he can use Sakon and Ukon's Kekkei Genkai to grow a mindless clone of everyone's DNA he has out of his stomach, from all the members of the Sound Four to Orochimaru himself!
Danzo's arm has ten Sharingan eyes embedded inside of it.
It gets worse when Danzo's chakra gets exhausted. The Senju cells in his shoulder go out of control and start to grow rapidly into a gigantic tree-tumor on his body. Danzo has to ditch the whole arm to escape it safely.
Itachi's genjutsu causes Naruto, among some other things, to see Sakura's head growing from his stomach, Kakashi's from his shoulder, half of his face and body turned into Second State Sasuke, and Gaara's eye and tattoo on his hand.
Sasuke's second-stage of the curse mark has bat wings which also looks like webbed handsgrowing out of his back.
Shino and the rest of the Aburame clan are all human insect hives, and to make it worse in Shino's first fight he beats Zaku by having them crawl up the air tubes in his arm (which themselves may be an example).
If Deidara's mouth-hands (including tongue) weren't weird enough, he has a third, bigger mouth on his chest.
Obito. Half his body was crushed so badly by the boulder he had to be permanently fuzed to a Zetsu to survive...
Princess Kraehe's transformation sequence in Princess Tutu, true to her role as the Dark Magical Girl, is incredibly painful, involving thorny vines wrapping around her to form her costume as her mouth is open in a scream. And then there's the second season, where Mytho is slowly transformed over several episodes into a giant crow. The transformation includes his shadow changing into that of his crow form, scenes implying that feathers are growing in under his skin (the episodes leading up to his transformation show him constantly scratching his arm) and him slowly taking on more and more inhuman mannerisms. As disturbing as the physical transformation is, though, it's nothing compared to the mental transformation he goes through, as he becomes selfish, obsessed with gaining others' love, and both emotionally and physically abusive, culminating in madness.
Urotsukidouji is absolutely MAD on this kind of Shapeshifting Squick. So bad that we need to put these in spoilervision. In the first film alone, a teacher turns into a demon with one big eye, a creepy looking tongue with another eye on it and rapes the lead girl. Nagumo goes through 3 transformations, each more horrific than the last, culminating when he is having sex with Akemi, turns into a demon while doing it, much to Akemi's obvious but silent chagrin, then growing to hundreds of times his own size. Nikki cuts of his own penis and replaces it with a demonic one, then later becoming something reminiscing Man-Spider.
The second film isn't too bad, though.
The third has a few but the worst of them all is when Ceasar reveals his robotic body for the first time, sprouting extra limbs and losing an eye which is replaced by a robotic one. Go figure.
Hell Teacher Nube is rife with these. Just a few examples from the vast gallery of the grotesque:
Nube's Red Right Hand (actually his left) which threatens to consume the rest of him if he loses control over it.
Another time, exorcising a demon that was taking over a child's body caused it to leap onto Nube, transforming him into horrific shapes.
Soul Eater brings us Chrona, who has a living being named Ragnarok mixed in with his/her blood who usually appears by making the top half of his body sprout out of Chrona's back. Ragnarok takes many forms over the course of the series, starting out as a musclebound humanoid figure and later becoming a dragon, a chibi version of his first form, and currently a form which has at least three arms.
There's also Asura, who has three eyes and "skin scarves" which are areas of his skin that he stretched out to ridiculous lengths so that they not only function as clothing, but also as prehensile tentacles which he shoots out of his back.
Asura's human form is actually pretty Bishounen. But before that, when he was reborn...
Soul's repeated dreams of bursting out of his partner Maka's body. No wonder he woke up screaming the first time...
Baddies in Burst Angel. People explode into monsters after going insane.
Naraku. He's a half-demon created by a swarm of demons merging with a single human soul. As a result, during his "night of humanity", he reverts back into a swarm of demons clustered around his human components. By the first time we see this, he has been heavily damaged by a holy arrow and forced to assimilate more demons into his body to replace the lost ones. Couple this with his experiments in fusing, separating and refusing demons in order to find a way to increase the powers of his specimens, a process that he has been refining for use on himself in order to someday expel the fragment of him that's human, and the result... his "night of humanity" sees him as a severed head attached by slimy... strings... of sinew and flesh to a massive pile of random pulsating, twitching, demonic bodyparts. In the early seasons of the anime, once he's actually confronted in the flesh, a favored form sees him as a human upper torso with myriad withered limbs sprouting from his back and a writhing cluster of misshapen tentacles and tails replacing his lower body. His "puppets" also display elements of this, in that they physically attack by taking the form of giant knots of tentacles protruding from the ragged remnants of a white baboon skin..
During his poison treatment behind closed doors, it takes only one quick peek for Bon Clay to conclude that this is perhaps a Fate Worse Than Death. And it's been going on for 10 hours, and according to Ivankov it takes 2 more days.
Perhaps not as disturbing but also qualifying as Body Horror is the draining of the moisture from his arm during his fight with Crocodile, resulting in a skeletal, useless limb with skin stretched over it.
Pumpkin Scissors has the 908 High Temperature Troopers unit of the "Invisible 9" program. Rather than scaling back the overly powerful flamethrowers they wield, or making the cooling systems in their suits work, the higher ups simply fill the suits with a special chemical that is one part artificial skin to one part anesthetic to one part burn lotion. Because of how well it works, the One-Eyed Cremators (to give them their Japanese Name) have no idea that the weapons they're using are burning the flesh from their bones. A veteran member of the 908 is implicitly nothing but organs within a shell of charred muscles and scorched bones, kept alive and unaware of what's underneath by their suits.
The first inkling the troops had that something was wrong was when they climbed out of the suit, laughing, joking and contemplating going back home — then noses, ears and skin started dropping off.
In Princess Mononoke the two boar spirits Nago and Okkoto end up like this, and it would apparently have been the eventual fate of Ashitaka as well.
In D. Gray-Man, when an Akuma disguised as an human shows its true form...
Suman Dark, or Allen pushing his arm too far, or the Akuma virus, or Level 0 Akuma forcing themselves down their hosts throats.
The Akuma blood bullets make you break out in a pentacle-shaped rash. Then you explode into toxic dust.
When Road stabbed Allen in the eye, we get to see his partially regrown-but-still-not-there eye-socket!
When Allen's arm was all flaked and looked like it was about to fall off. Then Tyki ripped it off and then had his Teez eat a hole in Allen's heart.
And Tyki phasing his hands through people's bodies, grabbing their hearts and ripping them out.
Almost payback for Tyki's Body Horror infliction on Allen: He transforms rather gruesomely into a demonic knight thing that turned the Black Knight scary again. He now uses weird energy circle things to trounce his enemies left and right. It also seems to have a taste for blood.
Chapter 195 is nothing but this trope when Alma's awakening triggers the Dark Matter cells in the 3rd exorcists to do this. It gets worse.
Guyver has a number of examples, but perhaps the best two are Sho's initial bonding to the Guyver unit before it develops its "exoskeleton", and Aptom. Thanks to the experiments conducted on him, he can physically fuse with other living creatures, absorbing them into his body to acquire their powers and repair his own injuries.
And because Aptom is kind of a bastard, he tends to do this while the Zoanoids he's absorbing are still alive.
Zoanoids disintegrate when they die. All of the zoanoids he absorbs are alive when he does it.
When the Jabberwock takes over Ryo's body in Project ARMS, the nanites across Ryo's body spread out and cover his entire body as a normal teenager is turned into a hulking engine of rage and destruction. The Body Horror can clearly be seen in Ryo's first full transformation, where his face is absorbed into the Jabberwock's chest.
Mon Colle Knights had two once the Mood Whiplash sets in. The first involves an angel in the process of falling, depicting horns growing out of his head and his back swelling up into a twitching fleshy clutter till his wings pop up and skin layers are flying around and then his new biomechanic wings tear out. Then the Terror Dragon already looked disturbed before, then it has a pandimensional creature incarnated into itself causing it to convulse, boil, new wings ripping through the melting skin, the head falling off and ultimately two new heads tearing through the back with blood spraying everywhere, all in high detail. Furthermore, once the transformation is over, if it needs to grow new limbs in self-defense, it will also bloodily rip through its own skin. The only reason this got to air on Fox Kids was that the blood was colored fleshy and not red.
They also toy around with the trope during one of Kurama's fights. His opponent releases a gas intended to transform Kurama into a baby so he could easily crush him. However, Kurama doesn't look to be in much pain during the transformation (besides getting a little woozy); but the gas has an unintended side effect, awakening Kurama's true form. It isn't all that ugly but the way his opponent reacts you would think it was a Body Horror.
The virus from the manga Emerging causes your body to bloat tremendously during your last few hours, to the point of ripping your clothes. This is likely due to the all the High Pressure Blood building up, which soon begins to exit from any orifice it can. Then your eyes melt, and your body rots from the inside... all before you die!
Copious examples in King Of Thorn. Infection by Medusa causes the body to slowly petrify and eventually shatter. If you're lucky, you might instead get a very nasty Lovecraftian Superpower. And then there's Alice, who has been reduced to a head, heart, one lung, and one arm, and kept alive inside a life support chamber for eight years.
In Chrono Crusade, a young human boy named Joshua takes the horns of a demon from the Big Bad and takes him as his own. The scene when the horns grow on his head is incredibly painful, showing the horns breaking through his skull with enough force that blood splatters the walls. Years later it shows that the horns not only cause him physical pain but deteriorates his mind, to the point where he can barely remember who he is. The manga version also has the demons who still have horns on their heads becoming corrupted and turning into mindless mutants at the finale. It's implied Joshua would have had a similarly gruesome fate if he hadn't had the horns removed soon after the corruption started.
The Kurosagi Corpse Delivery Service has plenty. Mostly from dead people, but sometimes the living too, such as when a snail parasite crosses over to humans. Said parasite makes the victim's eyes stand out on stalks - exactly like a snail's, in fact. Much worse than it sounds.
Or when they come across a company that is 'harvesting' an idol singer by growing ears on her - lots of ears. They're alerted by ghosts that grew a face on said ears. It's that kind of series.
Shakugan no Shana: Yuuji finds out, that he has the silver Tomogara, a giant knight, within him... By having it slowly crawl out of his body, while he's hovering in mid-air. The process is eventually stopped and reverted, but he suffers a Heroic BSOD after it.
As if poor RJ didn't have enough to deal with, what with his only friends being Ike and Clyde, his hand starts developing extra fingers and later an extra hand.
In the manga Oishinbo: Sushi and Sashimi there are lovely and horrifying illustrations of the possible parasites one can get from eating fresh water fish uncooked.
Claymore thrives on this trope. If a Claymore overuses her powers, her body undergoes increasingly grotesque mutations until she finally loses control and becomes an "Awakened One", a monstrously powerful demon. Add to that the fact that every Awakened One is unique (Outside of identical twins) and you have a whole cesspool of this trope. Just add the violence levels and the abilities some Claymores have developed just from coming close to awakening and you've got about as much as a series can handle.
That doesn't add the fact that the halter tops they wear apparently conceal something so horrifying that it has yet to be shown in any format (And with all the gore that the series is fond of, not showing something is Serious Business). In fact, Claymores are the only women ever who can stop themselves getting raped by showing off their nude bodies. Some would have you believe the space between their breasts is a mass of open sores, others think it's a youma's head grafted there.
The Eclipse Infection in Magical Chronicles Lyrical Nanoha Force. If you're lucky like Tohma, you get a Viral Transformation that gives you a whole slew of superpowers and a Super-Powered Evil Side that's a danger to your friends. However, if you're unlucky, like say... the piles of test subjects that came before Tohma, you get the chance to watch your body mutate in wild and grotesque ways before you burst open in a shower of blood and/or are reduced to lumps of flesh. Remember those alien-looking brain things from Chapter 1? Those used to be humans.
JoJo's Bizarre Adventure, and how. Possibly the worst happens in Stone Ocean. Father Pucci was having a rather off episode as a result of fusing with the bone Dio entrusted to him. He is walking through a supermarket, and inadvertently and randomly affects the internal clocks of different stuff in his vicinity. Eggs start hatching into misshapen chicks. A portion of an infant's face (head?) ages to adulthood. It being unintentional really makes it that much worse. What was that all about anyway? He still had his same old powers, and it never happened again... Although later on Pucci does safely implode his head momentarily with his new stand.
The Pillar Men are Body Horror incarnate, able to twist and contort their bodies in impossible ways (Santana is able to climb through a tiny air shaft by crushing his skeleton until he fits,) use ribs, arteries, etc. as weapons, and even climb inside people's bodies.
Makai Kishi Ingrid's villains are distinctly lovecraftian. One guy's got at least three Naughty Tentacles growing out of his shoulders. Combined woith his only expression being a demented, Mad Eyes leer, it goes from your average "heroine gets captured raped, and generally degraded like no tommorrow" Fan DisserviceHentai, and becomes even more horrific.
An in-universe version, and only to the two protagonists of Wandering Son. There's nothing wrong with their bodies, but being transgendered they think of puberty as this.
Kite Liberator, sequel to the infamous Kite, has the main character's astronaut dad transforming into a twelve-foot monster made of solid bone.
Blue Exorcist has a very nasty version in episode two, is which we get to see the effects of possession. Fortunately, they opted to make it slightly less horrifying than the manga. Urgh, his fingers...
Manga artists such as Jun Hayami, Shintaro Kago, Junji Ito, Suehiro Maruo, and Benko Tamaoki frequently depict body horror in their stories.
Crops up a whole lot in 3×3 Eyes, maybe most horrifyingly when it comes to the Hyouma Tribe and pregnancy...
Sengoku Youko sees Ax Crazy Resshin being modified countless times until he becomes in Yazen's words, "nothing more than a heap of trash glued together" and Senya, a young eight year old boy with a thousand demons living in his body.
Toriko gives us Bogey Woods, a man with 4,000 bones and 4,600 joints, allowing him to twist and contort himself in inhuman ways. And a favored technique of his is to enter the body of another person and wear them like a 'shell', controlling the lifeless corpse like a puppet through use of his inhumane skeletal system.
In A Certain Magical Index, one of the members of GREMLIN, Marian Slingeneyer, is able to reshape anyone who comes into contact with her gold tools into whatever shape she wants and keep them alive. Anyone who crosses her risks either a Cruel and Unusual Death or becoming the latest addition to her furniture collection.
Accelerator does this when he's feeling particularly vengeful. His preferred method of messily ending someone's life? Stick a finger into a wound, and reverse the vectors of their blood flow, causing all the blood in a person's body to rip itself out of their skin.
Happens to Madoka from Puella Magi Madoka Magica, when she steps into H.N. Elly's witch barrier and said witch has her familiars stretch her body to her limit as she pulls her inside. Complete with Mind Rape as she also mentally tortures Madoka via replaying Mami's Cruel and Unusual Death in nearby monitors.
Many of the Witches seem to have a thing for bodily mutilation. For instance, Izabel (the Artist Witch)'s familiars incorporate pieces of their victims in her artwork, and in just the first episode, Gertrud's familiars discuss (in distorted German) tearing up Madoka and Sayaka and presenting the pieces to their mistress. In the spinoff mangas, Arzt Kochen (literally German for "doctor cook") is a surgeon who removes organs from her victims while they're still alive, then cooks them.
The movie Biohunter wears Body Horror as its hat, dealing with a virus that mutates its victims into ravenous monsters. The first scene in the anime features a sex scene where a woman's breast grows teeth and eats a man's hand. Vagina Dentata was thankfully averted.
Many of the Asura avatars in Popcorn Avatar have this as their schtick when they transform into their "strengthened" form.
In Detective Conan, there's the part where Shinichi is shrunk into the body of a child. Smoke comes out of his body.
Shinichi (clearly freaked out): My body... it's hot!! Like my bones... like they're melting... no... no good...