Mortasheen's most notable inflictor of this is Willoweird, a nasty walking tree that hypnotizes you into eating one of its fruits. When then converts you into a tree, that the Willoweird then parasitically feeds upon. Did we mention that you can survive for decades in this state?
Both the old and new Vampire games (Masquerade and Requiem) had a variation on this. When Vampires are staked or starve for long enough, rather than dying, they are sent into torpor, a kind of stasis. This is far from mercy, as vampires in this state experience time more or less in realtime, but suffer terrifying nightmares. And considering that very few kindred would willingly starve themselves into this kind of state, this probably means that said vampire is trapped somewhere, meaning that this state can go on indefinitely. No wonder a great many ancient vampires (and possibly the antediluvians and Caine in the original series) have been driven utterly insane when revived.
One sourcebook mentions that the nightmares tend to involve what put you into torpor in the first place, with kindred starving to torpor stuck in an eternal loop where they hunt a human and never reach them. Go into torpor through violence, or being staked, and God help you— because you're going to relive that losing battle until someone finds it in their dead heart to revive you. That is, if they don't decide to chow down on you instead, in which case, you'll simply scream inside your immobile body and watch as your saviour devours everything that made you who you are and all your memories, before you crumble into a pile of ash. And that still doesn't end your torment, because it is rather heavily implied that you survive within your devourer's body for the rest of eternity.
Requiem somehow manages to make it worse; when you go into torpor, your memories tend to... shift. It's not uncommon for an ancient vampire to come out of a long torpor wondering what really happened, what was a story he heard second-hand, and what was just idle fantasy. Oh, and it's suggested in some books that vampire souls actually manage to travel to the Underworld when they're in torpor... and there are things in the Underworld that don't like them.
The Tzimisce in Vampire: The Masquerade do this for kicks to whoever screws with them, and a few who don't.
In the sourcebook Mexico by Night there is a character description of one Jaggedy Andy who, as a mortal, insulted Sasha Vykos, the infamous Sabbat Tzimisce. When Andy spit in its face, Vykos just simply smudged its hand over the mortal's face, crafting bone and flesh over all his facial features. Just as he was about to die, Vykos made one of its thugs Embrace him. Now he wakes up every night without facial features and every night he must open his mouth and eyes with a hammer and chisel, which is a very painful process. To add to the insult, he is as good as grounded to the landfill in which he was left, because even poking his face outside could start an uproar both among Vampires and Mortals. Another thought to go through before messing with the Tzimisce...
Similarly, the Hierarchy in Wraith The Oblivion does this to whoever causes too much trouble. Their ghostly corpus is "soulforged," boiled down and rendered into a permanent shape, be it a sword, a coin, or an ashtray. However, official word as of the 2nd edition is that Soulforging destroys the consciousness of the ghost being soulforged.
Changeling: The Lost does this to all changelings — your player character is someone who, by whatever scraps of luck, managed to somehow escape. And you have no idea if maybe, just maybe, you were actually let go. You may have been the pot in which a twining, bloodsucking rose was grown, your Keeper gently watering you with arcane acids and admiring the beauty of the flowers growing out from the slits in your lungs. You may have been twisted to have the body of a hound and the mind of a man, then the body of a man and the mind of a hound, over and over and back and forth until you couldn't tell which was which. You may have had to spend a hundred years walking along the razor edges of a network of swords, suspended high above a valley of crackling flames or gnashing rocks. The True Fae have such a wide variety of ways to "play" with humans...
In Mage: The Awakening, if an Abyssal entity doesn't simply kill you in horrible fashion or corrupt the next seven generations of your family to its service, it will likely inflict this upon you. Abyssal creatures are less than pleasant.
Demon The Fallen defines Hell very succinctly. Imagine you could see every single dimension - all of them. You can see all the colors in the spectrum, every atom in every mote of dust... You are a being of all of reality. Got that? Shut that all off in a fraction of a second. And then keep it off. For millennia. It's just you, the others who were on your side, and the thought that everything you worked for has failed and can never be regained. Yeah, there's a reason the DemonKarma Meter is called Torment.
This trope nicely sums up the Warhammer 40,000 universe. And then there are hundreds of orders of magnitude nadirs that really stand out...
There's the God Emperor of Mankind, the Messianic Archetype of the setting. Reduced to a shattered husk, kept on life support for 10,000 years (powered by the lives of 1,000 psyker every day), unable to move or communicate yet his living consciousness is used as a psychic navigation systemfor Faster than Light travel through what is basically Hell, and also while the unified humanity he worked to build falls into a dystopian hell around him. It gets more into it when you realise that everything he aspired to accomplish (secular humanism and the destruction of Chaos altogether) is being defiled and torn down by the Corrupt Church. In his name. On top of that, the supposed preachers of his word are also the ones possibly conspiring to keep him in the vegetative state, as they're all paranoid and believe that if he is allowed to die and reincarnate, he'll be gone forever and the Imperium will plunge into darkness forever (Inquisitor Lord Karamazov was famous for executing one of the supposed "reincarnations" of the Emperor, much to the chagrin of his collegues). A quote about the 40k universe sums it up:
"A galaxy where the only person still sane is powerless to do anything but watch the universe die."
According to the Inquisition War trilogy, he actually is still conscious and aware of his status on life-support, and still somewhat capable of psychic communication to anyone in his closest vicinity and freezing time to that person if he so wishes. It is heavily implied, however, that he cannot focus too much attention to communicating with anyone who he is talking with, or he'd not be able to handle the most vital parts of the Imperium, such as the Astronomican.
The Inquisition War trilogy also details the continuation of consciousness whilst suspended in a stasis field, though the consciousness is locked in whatever feeling was being felt at the submersion in the stasis field. Naturally this discovery is then used by the Inquisition to torture individuals for great lengths of time while effectively halting the decay of their bodies.
Hey, that means that Roboute Guilliman, Primarch of the Ultramarines is experiencing this. Mortally wounded by a poison blade wielded by his former brother primarch Fulgrim, the Apothecaries bundled him into a stasis field while on the verge of death and set him up as a shrine (something he would likely not appreciate). Ouch.
People near death release endorphins to dull the pain he iss actually probably been high as a kite for the last 10000 years.
Again, point of view is everything. Guilliman is serving as inspiration to his chapter and their many many successors. While he might be suffering (but thats quite a noble thing in the Imperium), he is also watching over his sons as they fight for the Emperor as he did. Even in their darkest days, Guilliman is standing vigil...
A spinoff short story Into the Maelstrom has a traitor Space Marine imprisoned in a Dreadnaught battle suit, normally an honor, but never released, so he is doomed to live forever in a small metal box, with no limbs. This is in fact the fate of all Space Marines encased in Dreadnaught armour, with the occasional mindless rampage, but it isn't always this trope (and is a good example of how a different attitude can affect the outcome). Regular Space Marines, both those encased and their brethren, consider it an honour as they can fight the Emperor's enemies even after death, albeit with slowly degrading mental faculties. Chaos Marines however, being Sense Freaks taken to the literal utter screaming extreme, consider it to be the worst punishment imaginable, as even while battling they can't feel the joy of slaughter and while inactive their brethren have to chain them to a wall to prevent the completely bugfuck insane Marine (even by Chaos standards) from breaking loose and killing everyone.
Chaos Dreadnoughts were purposely built with this in mind, their sarcophagi reconfigured to drive the occupants into madness, which the occupants can never get used to because of the design.
Any Daemon Weapon or a bound Daemon results in this on a Eldritch Abomination. The daemon is so crazy that he will attempt to devour its wielder just so it can get some sort of outside contact, even though such an act would result in the weapon being rendered inert again.
Fulgrim has an impressive one of these, as the primarch Fulgrim is eventually completely possessed by the demon joyriding in him, who keeps him fully aware of its actions in his body, which is mutated by the demon into something more pleasing to it. While his soul was trapped inside a portrait. As this occurred during the Horus Heresy, the fate is up to 10,000 years and running.
Not necessarily; Horus vowed that he would free Fulgrim from that particular fate, and there's a chance he managed it before dying. We'll have to wait and see.
Then its revealed that Fulgrim had successfully regain control of his body, and he trapped the deamon in the portrait he was trapped in, and is fully embraced his new form as a Daemon Prince.
The primarch Lorgar spends his entire time thinking about the true nature of Chaos.
Haemonculi do this to their victims, surgically altering their bodies until they are, say, a collection of organs still alive and sentient, or a sack of helpless flesh. The Haemonculi arts, however, are in fact required by the Dark Eldar to survive (pain and the suffering of others apparently grants them immortality so that they in turn do not suffer And I Must Scream under Slaanesh). Needless to say, this may very well apply to every single slave of the Dark Eldar.
In Nightbringer, the Ultramarines find a victim of a Haemonculus on Pavonis that was entirely dissected and hung piece by piece like a blown-apart cross section of a human being. Then they see that the various pieces and organs of the victim are still connected by veins and nerve strands. THEN they realize the victim is still alive and feeling every agonizing moment, and is trying to rasp "kill me" at the marines. It freaks the fearless Ultramarines out so much they open fire and euthanize everything in the vicinity to splinters. High octane nightmare fuel indeed.
The Eldar as a whole. Once Eldar die, their souls are still fully conscious in the Warp and then immediately sucked into a hellish disgusting vortex by Slaanesh to eternally torture and rape them in countless different ways day and night forever and ever. Thus it is completely necessary for them to make gut-wrenching sacrifices, including manipulating entire civilizations into destroying each other (and in the case of the Dark Eldar, torturing other species as sacrifice to appease said god of pain), just so that they can save one of their own. All Eldar need to carry with them a Spirit Stone (or Waystone in some versions) that absorb their soul upon death, preventing Slaanesh from getting his hands on them. These same stones can be used to revive them in the form of a Wraithguard or Wraithlord or (in the case of farseers) put into the craftworld to join a crystal wall of seers for all of eternity, sharing their knowledge with their descendants. However, it's known that several craftworlds are desolate and completely devoid of life, as well as eldar falling on foreign worlds, their stones remain unretrieved for possibly many years, or never. They will be stuck alone, unable to communicate with anyone (it's stated that they only join their ancestors once their spirit stones are attached to the infinity circuit), for all that time.
A similar fate happens to Exarchs. These are warriors who are lost upon their path of war and unable to leave it, becoming instructors to others that want to learn the art as well as leaders in war. Each Exarch, upon death, would merge with their suit rather than their Spirit Stone, so that they may once again join the next generation of warriors when their suit is donned again (they merge spirits with whoever wears the suit). Phoenix lords go through the same thing, except that their personality completely dominates the other souls. Much like the Spirit stones, it's implied that many exarch, and some phoenix lords, now lay on some forgotten world, their suit lost forever and unable to communicate with anyone.
Still nothing compared to the Outsider and possibly some Necrons - they were imprisoned before humans ever arose, on the order of some 60 million years. When awake the Necrons fall into this trope, completely subservient automatons trapped within effectively immortal metal shells. Most Necrons are "fortunately" mindless and probably not aware of their situation, but Necron Lords most definitely are.
Almost the entire Thousand Sons Legion suffers from this, as a screwed up spell caused most of them to be reduced to dust with their souls trapped in their armour. They can still move (and fight) but are utterly enslaved to Ahrihman and the other non-dusted leaders.
One of Slaanesh's circles of temptation is filled with fantastical treasures. Anyone who touches one of the golden statues will be turned into gold himself, while his soul remains fully conscious.
Speaking of Slannesh, there's also his champion, Lucius the Eternal, a complete monster by many people's standards (Even his fellow Chaos Space Marines consider him a monster amongst monsters), who cannot die. To be specific if, by some rare chance you do kill him, if you feel the smallest amount of satsifaction for your deed, you will ever so slowly be transformed into Lucius. Eventually nothing will be left of you, except for a new , throbbing face with an eternal scream fixed onto it on Lucius' armor, and in the 10,000 or so years that he has been killing (And been killed) he has dozens, if not hundreds of those faces covering his armor.
In the new Necron codex, there is mention of a crownworld where an alien prophet's head is kept alive in stasis to predict the future. It's implied to have been stuck there for the past 60 million years.
There is also a daemon that was banished and trapped within its own skull by the Grey Knights, and is kept in that state by the constant chanting of acolytes.
The Grey Knights' Vault of Labyrinths has several dozen Soul Jars that contain daemons trapped inside them.
A milder example occurred in the short story "Among Fiends". The Chaos Champion Scaevolla is forced by the gods to choose between hunting down the progeny of his former best fried for all eternity or spawnhood. He isn't pleased.
Warhammer Fantasy has Count Mordrek the Damned, which under normal circumstances would be a redundant title for any Chaos warrior. This one suffers from constant and horrific mutations, but unlike most that suffer this fate, he remains sealed inside his armor, and his mind has been left intact. It's also mentioned that every time he dies the Chaos gods resurrect him, and this has been going on for so long that no one remembers which god he worshiped, or what he did to offend them.
Dungeons & Dragons has the Imprisonment spell, which entombs the subject for an indefinite amount of time somewhere "far beneath the surface of the earth". Normally, this spell is not an example as the victim is put in Suspended Animation and won't remember any part of its imprisonment when released. However, in Baldur's Gate this is not the case as the player is threatened with this spell (and the emphasis of suffering) by a Harper, and one can free a number of people from an artifact that imprisons users in the Underdark; all but two (one who'd only been in there for days, and another who was The Undead and presumably too crazy to be affected) are alive but incurably insane.
The supplement Book of Vile Darkness has the spell Eternity of Torture.(Like most Vile Magic, only wizards who had already fallen past the Moral Event Horizon would consider using it.)
Dungeons & Dragons' Ravenloft setting has a monster known as the Wall of Flesh. It's created when the rage and fear of a person who has been imprisoned within a wall mixes with Ravenloft's special flavor of magic.
Several named NPCs of the Land of Mists have likewise suffered an And I Must Scream fate. Elise Mordenheim, trapped in a decaying and shattered body that her Mad Scientist husband struggles in vain to restore, is perhaps the most prominent example.
One Dungeons & Dragons monster race, the Aboleth, are immortal abominations of the sea. Should they dehydrate, they don't die, but instead turn into an immobile shell, still aware but incapable of any sort of action. This is described in the Lords of Madness supplement as a Fate Worse than Death.
The Transmogrification spell from GURPS: Magic keeps the target's mind intact and active but makes them in to an inanimate object for a while. The Entombment spell traps the target in a tiny bubble deep beneath the earth for eternity unless it is somehow undone.
Exalted, like Wraith The Oblivion, has soulforging as a common practice in the Underworld. It goes past "common" — soulsteel is considered one of the five magical materials, and the Deathlords are all too willing to make their undead subjects into arms and armor for their Abyssal soldiers.
Made worse in that soulsteel was around before there was an Underworld. Autochthon, the great maker, had a race he made that pissed him off so much that he melted their entire civilization into slag and removed all references to them, and THEN took their souls and forged them into soulsteel inside his body.
The Ebon Dragon has Charms that allow him to banish victims to a horrifying darkness beyond reality where they are completely alone and from which there is no escape.
The Neverborn, who are simply too powerful to die, are locked in an eternal nightmare from which there is no obvious escape. This is how they can be sympathetic despite their plan (insofar as they are sane enough to have one) being the complete obliteration of everything that exists - because this is quite possibly the only way for them to finally escape.
Ravi, a planeswalker in the world of Ulgrotha, was desperate to end a huge war. She did so by ringing the Apocalypse Chime, which wiped out the whole battlefield of its warring parties, and put herself in a magic coffin designed by her mentor to avoid the destruction. Unfortunately, she didn't ascertain how to get OUT. She was eventually found by Baron Sengir, becoming the "delightfully" mad Grandmother Sengir.
In Burning Empires, infection by a Vaylen is treated much the same way as character permadeath because the infected character is irreversibly rendered unable to control its own body, effectively comatose, even when there's no worm driving it around.
In Monsters And Other Childish Things, the empty skin of a person an Excruciator has hollowed out into a Living Bodysuit is explicitly mentioned to be still live and conscious. No, the game doesn't even hint that there's any way to restore a person from this.
The canonical fiction of Cyberpunk 2020 has Alt Cunningham's personality/mind transfered into cyberspace by the evil Arasaka Corporation. When the connection to her lifeless body is severed, she becomes permanently trapped in there: "Behind the walls of monitors, a disembodied Alt screams to [her boyfriend]".
While the Immortality gift from Nobilis explicitly protects you from attempts to pull this, this doesn't stop it being played straight in some of the border fictions.