In Human Curiosity, it's theorized that the frozen nations are experiencing this, leading to Liechtenstein wanting to speak to Switzerland's body. Subverted in that when France recovers from having been frozen, he could not remember any of that time.
Not all the Nations who died in the 1983: Doomsday Stories passed on right away when the bombs fell. Some managed to stay alive for some years after, though more as a Body Horror that's slowly falling apart.
Kenpachi's zanpakutou in Sight is described as being constant agony and is screaming with no one able to save him and his wielder can't save him because he can't hear him. The zanpakutou disturbs Ichigo greatly, but he can't do anything about it.
The people whose minds Kodachi Kuno of Divine Blood devours in order to take over their body as part of her collective are eventually shown as having fragmented pieces of their mental identity remaining in her collective mind as well as their entire souls enslaved to her will. When she manifests in a mindscape shortly before finally being exterminated, the mouths of the multitude of people she'd devoured are shown to be either gagged, sewn shut with needle and thread, ripped out or simply not there.
In Waking Nightmares, Celestia does this to the Zompony Grey Hoof. Not only was he imprisoned in the ruins of his home, Sunnytown, but a fear spell was placed on the land, one that causes all forms of life (including plant life), to flee in fear and become too afraid to approach. In addition to this, the town itself was shifted into a pocket dimension, and he was rendered unable to go insane. He's cursed to be alone forever, with no escape...
In the Horseshoes and Hand Grenades story, A Month of Sundays, Quetzalcoatl states that he was trapped underneath the remains of an ancient Aztec Temple for 500 years, screaming and begging for someone to help him.
In Opening Dangerous Gates, a Tengu removes all five senses from the party. Lucy almost goes insane, but realizes she can still move and her keys must still be on her belt even if she can't see or feel them. With a bit of effort, she manages to grab the white key and summon Ulquiorra, and the sheer reiatsu released by his arrival dispels the effect.
In Super Sentai Vs Power Rangers The Liveblog, main villain Radiguet has the Scouts' souls trapped in the elemental stones of the fallen monsters, and the energies from it make the heroes vessels for the new souls, turning them into the Fallen Scouts. Every time a Fallen Scout uses a powerful attack, a part of the original Scout's soul vanishes, much to the horror of the All-Stars. The Scouts can do nothing but watch as they are forced to fight their friends and transform into hideous beasts, but they later gain the strength to break the spell.
In The Bridge, Monster X spent about 72253 days, or 198 years, entombed within the giant asteroid Gorath, with only his own voice and nightmares for company. He didn't go insane, but by the time he was released, he had lost all his memories. His Super-Powered Evil Side Kaizer Ghidorah has it even worse. Whenever he's not in control, he's trapped inside a cage deep within X's mindscape, but aware of everything.
Gendo and all SEELE's members fates: Their souls were ripped from their bodies and imbedded in the walls of the properly named Hall of Torment, where they'd remain trapped for all eternity.
He was at the Hall of Torment. The senior members of SEELE and his father were imbedded in the walls, ceiling, and floor of this place, screaming in agony, their souls trying to claw their way out of membranes of unreality that would trap them for all eternity.
Later on, the Chaos Gods would use this same method to punish child abusers and human traffickers.
In the series Lex Luthor Triumphant, Lex Luthor traps Superman, keeps him powerless with a combination of red sun rays and brain surgery. He develops an interface that allows him to control Superman's body and has him kill Lois Lane, after she finds out he captured, lobotomized, skinned Superman, and that selling his eye, skin, teeth, and fingernails has made Luthor even richer than before.
In the Teen Titans Saga, this is Veneficus' ultimate fate, as he is trapped in the void between dimensions with no means of escape. And since demons appear to be immortal barring being killed by someone else...
Fanfic ''Plaything of the Gods'' focuses on this happening to Light. He learns that the Shinigami King has come to Earth and he's told by Ryuk that the King is looking for him. Light sets up the stage so that he can meet the King and become more powerful. What Ryuk failed to mention was that the King will violate his body. Multiple times. He spends weeks being drugged and raped by the King and is practically begging for someone to help him. What truly makes this horrifying is that he gets sealed in by the task force and is going to spend years as the King's sex toy. But hey, at least he'll be powerful like he wanted.
Never Had A Friend Like Me: When the Pixies and the Anti-Fairies attempts to kill Timmy and Amanda, Norm who was watching and has grown attached to Amanda, does not take it well. After Amanda wishes that the Pixies and Anti-Fairies couldn't try to do this again, Norm traps them in a pocket dimension indefinitely. Of course, Norm might come around and ask for a favor from them for good behavior, but it fits.
In Need for Control, Hojo had put Vincent through this as a method of torture that left him unable to function as a 'free' human being:
Vincent: "After my arm was removed, I was rendered unconscious again. When I awoke, I had no idea where I was. I found myself in the dark, unable to move. I couldn’t feel my body or hear anything. Even the air around me seemed to lack any type of smell whatsoever. At first, I found this to be a relief, thinking that if nothing else, that I wasn’t being tortured. However, that complete lack of external stimulation began to do something to me. Time seemed to have stopped, and I had no idea of how long I had been in there. I began to wonder if I was even alive… Not being able to feel, see, or hear anything does something to you after a time. I began to long for the torture. At least when that had been happening to me, I knew that I was alive."
However, that's not even the worst of it, as it's stated that all the time that Vincent was in the coffin before you find him? He's in that state. Twenty-seven to thirty years of it.
Vincent: "He put me back in the dark…I never even knew what it was that I’d done wrong… He just put me back in the dark and forgot about me… Twenty-seven years, Cid… I was in there for as long as I had been alive before Hojo had put me in there…"
In Off The Line Vincent is trapped in a virtual reality game for 15 years where he can never sleep or let his guard down without risking being killed by players or the game's moderator and no one until Rainstorm had ever realized that he was a person. As a consequence his mind is a wreck and he can't remember anything outside of his own name because he never had the chance to rest, thus he couldn't properly process his memories.
In Eirs Tommorrow, during the Apocalypse How and death of his original timeline, Cloud cannot die and has to watch everyone he loves, his home and the world die and he could do nothing to change anything.
In At Gates Edge when Edward died and became a ghost, he has been trapped in an office, unable to look outside and unable to be seen or heard by anyone for seven years. But this changes when Roy is able to see him.
In The Prince of Gryffindor Harry turns Voldemort into a jellyish goo and traps him in an unbreakable, unopenable jar, then throws it through the Veil of Death.
Another fic (can't remember the name) has Harry managing to sabotage Voldemort's rebirth ritual by throwing all kinds of random stuff like twigs into the cauldron. The result is an immortal blob of flesh in the shape of that very cauldron, and without any distinct external or internal features. The Department of Mysteries keeps it, but never manages to figure out what it is.
The Kin of Fan Fic/Hivefled are the ghosts of trolls tortured to death by the Grand Highblood, trapped in a metaphysical dark room for thousands of years and potentially forever. They still carry the wounds of their death, which may still hurt, and the Highblood can come in and make more use of them any time he feels like it.
At the end of Night of the Mannequins, Gaz is turned into a store mannequin after sneaking into the mall at night to be first in line for the new Game Slave 3. Worse still, she's put in a display window directly across from the store selling them, and it's strongly implied she's still aware.
In Virtual Reality, Real Terror, a group of students and teachers — sick of Gaz's constant bullying (which she gets away with because of her father) — hire an entity known as the Exile to deal with her. It does this by absorbing her into itself, wherein she's kept alive indefinitely, but unable to move or speak (or, in keeping with this trope, even scream), and forced to experience first-person recreations of every act of violence she's ever committed against anyone else.
The works of HeCallsMeHisChild feature a species of shapeshifting, blob-like predators called Morflar, which feed on Irkens. Once absorbed, the Irkens are robbed of movement and every sense except tactile feeling, which means they can't even scream as all they feel is themselves being digested (and due to the Irkens' Healing Factor, this process takes about a century). In two different continuities, this fate befalls Tallest Red.
In Invader Zim The Series, this is the final fate of Zoburg, crucified to a rocket and shot into orbit, but with his pressurized armor keeping him alive indefinitely.
In Queen of All Oni, after Jade transforms and brainwashes Viper into Hebi, the latter explains that Viper is trapped in her own mind and unable to stop her new persona. A scene in the seventh interlude shows this from her perspective, and it's a never-ending nightmare of being crushed and bound, with no sense of self or time, with only the briefest glimpses of what's happening outside.
Link Sr was sealed alone in the Fierce Deity mask for almost a century. He describes the ordeal as "goddamn annoying". Subverted by the fact that he canand does free himself without help, it just takes time.
Magi is considerably less fortunate. As punishment for ordering Link's people and family murdered just to get to him, he is chained in a Sealed Room in the Middle of Nowhere for roughly a decade while insects devour his honey-covered, disembodied heart over and over again.
The goddesses are implied to suffer this after Link awakens as the God of Fear and chains them to Fate and Destiny's former throne, but no details are given.
Link himself suffers this during his four seven-year naps when the goddesses see fit to send his mind through the Ocarina of Time adventure "about 3,500 times give or take a few hundred, each year, and in each timeline" for a total of 98,000 times over 28 years all for the purpose of refining his instincts to create as powerful a warrior as possible. They even had to tinker with his mind by building a "wall" around those instincts to contain them.
In one alternate ending to the infamous fanfic Cupcakes Pinkie Pie, unable to cope with the guilt of what she did under the influence of a Parasprite, voluntarily submitted herself to this via Taken for Granite.
Twilight Sparkle spends the first portion of the story trapped in her own mind, forced to watch as her Superpowered Evil Side, Nihilus, repeatedly tries to kill her friends.
Nihilus in turn does this to Rainbow Dash, subjecting her to a Mind Rape spell called the Insanity, which changes her into an insane, nigh-amnesiac berserker who serves as Nihilus' Dragon, with Dash stuck inside and tortured if she tries to fight back.
A flashback shows Titan apparently subjecting Discord to this (we only get vague details about it) after Discord caused the death of Titan's son. It's strongly implied that Celestia and Luna's defeat of Titan is what allowed Discord to escape. Though to be fair, Discord is considered the Lesser of Two Evils between him and Titan to the point the heroes actually free him to form an Enemy Mine against Titan.
Dinky's fate in the Bad Future was to be turned into a filly-shaped muffin. When she's restored by the Elements of Harmony a thousand years later, it's revealed that she was completely aware of everything the entire time.
Also in the Bad Future, it turns out this was Fluttershy's fate as well. Fluttercruel, like in the main timeline, is a separate entity from Fluttershy who was granted control of their body. Unlike in the main POV verse, however, Dark World Fluttercruel remained in control and was raised by Discord instead of Fluttershy, becoming an even bigger monster than him, while Fluttershy was forced to watch all the horrible things she did. And on top of that, it turns out Fluttercruel liked to torture Fluttershy in their mindscape for fun. Fortunately, Cadence's spirit eventually managed to save Fluttershy's soul, though only after five hundred years of all this.
Turns out, even Discord himself was subjected to this in Dark World. Nightmare Paradox has kept him trapped in a "Groundhog Day" Loop that always ends in the deaths of his daughter and himself for somewhere in the equivalent of a few hundred million years. It's so bad that when he gets Dragged Off to Hell and horribly killed by his family for his crimes over a billion times, he doesn't mind in the least, as it's relaxing compared to what Paradox put him through.
Sweetheart's little sister Cream ended up suffering this in Sweetheart's 7 Dreams/Nightmares story. The shock from the explosion that destroyed G2 society ended up "locking her in", meaning her body was paralyzed to the point she couldn't even speak (worse, this is a real condition), but she was completely aware and conscious of everything. Including being dragged off and torn apart by mutants created by the explosion, taking this trope literally in that she literally couldn't scream. Worse in that because of her condition, they may simply have went straight to eating her alive.
In the Shining Armor Arc, it turns out that Makarov'sAlicorn Cyborgs were all ponies he abducted and forcibly transformed. Now they're trapped in their own twisted bodies, unable to stop themselves from killing at his whim.
In "Character Rerailment", Silver Spoon becomes trapped in a nightmare where she's forced to live through the events of the episode "One Bad Apple", unable to control her body and forced to watch and listen as herself, Diamond Tiara, and Babs Seed make the Cutie Mark Crusaders (who had become her friends earlier) suffer. She eventually finds the strength to break free.
Silver Spoon's thoughts: Daddy! Something's wrong with me!...Listen to me daddy! Please! I'm not happy! I'm scared! Can't you see that?!
Silver Spoon's thoughts: I want to cry...But I just keep smiling...
At the end of the Wedding Arc, Cadence — now the Queen of the Changelings — does this to Kabuto, Chrysalis' sociopathic Mad Scientist. As punishment for his countless crimes, she has him sealed insidethe sun, completely aware and in agony, for a length of time no less than the number of years equal to those his victims might have lived. He'll be there for several generations, at least.
Ironically, in the same arc Fluttershy reinstates to the interviewers that this is what Celestia would've have done to Fluttershy in a fit of rage had Nightmare Whisper fiasco ended with the deaths of thousands of unborn foals.
Some of the Mane Cast in Sweetie's Mansion is this when they temporarily become Sweetie's Spirit Advisor to help her defeat their ghostly selves whenever she takes a picture of one. Luna on the other hand is well aware that her spirit is under the control of Specter but she can't stop herself from attacking Sweetie Belle, Luna can only warn her what her ghostly self is about to do like the mane cast who became Spirit Advisors for Sweetie.
In Pages Of Harmony, after Twilight Sparkle kills the other Elements of Harmony, they don't move on to the afterlife. Instead, they're trapped in a limbo-like state where they can see and hear Twilight, but she can only hear them. And their Mind Raped personalities are still intact even after they die.
Plenty to go around in The Conversion Bureau: The Other Side of the Spectrum. Due to it being a DeconstructiveHate Fic to the TCB genre (especially the works of Chatoyance), it's a given that ponification is this. The author Redskin 122004, however, went above and beyond in making it horrifying though, and they're frequently referred to as perpetuallysmilingzombies on the tropes page and among the fans. The single crowning moment of Nightmare Fuel for them, however, has to be the fact that the human converts' souls are literally broken to pieces and bound to Queen Celestia and Tirek's will. Even worse, according to the Zebra shaman Quagga, it is utterly impossible to repair said souls; only death will make the newfoals' souls whole again. Meaning even if the Queen and the bag are defeated, only masseuthanasia will set their souls free.
Marcus (describing the potion): "Rewrites a person into a pony... changes their body, their mind, binds their soul in chains... takes them away from you."
The Wham Episode chapter For Whom the Bell Tolls reveals that this is also the case for the TCB Universe's Mane Six. When Canon!Luna fishes around in TCB!Twilight's mind to gather some information, she discovers that Queen Celestia personally Mind Raped each of the girls by imprisoning them in their own minds and then implanting evil new personalities to drive their bodies around to carry out her will. All the TCB!Mane Six could do over the three long years of the war was helplessly watch on as their controlled bodies commit Moral Event Horizon grade acts against the humans and other species of Equis. TCB!Twilight herself is reduced to a horribly broken and sobbing wreck who desperately begs Luna to kill her already and stop the madness.
In The Elements Of Friendship, Trixie's soul is half devoured by the Alicorn Amulet at the end of Book IS, leaving it trapped inside her comatose body, begging for death.
Trixie has a nightmare where she's unable to move, speak, or scream while Gear Shift, Cover Story, and a mysterious stranger order her chest cut open with a machine right out of an alien abduction story. She eventually guesses that it wasn't a dream, but a memory.
Gear Shift and Cover Story brainwash Lightning Dust into a minion. When the Mane Six and Trixie manage to free her from the control, she reveals she was aware the whole time, a prisoner in her own body.
In the fic Two Moons, Deidara's soul is removed from his body during a fight with Orochimaru, and takes up residence in the back of Itachi's head. Fittingly, Deidara isn't pleased (he actually does scream for quite a bit), and is completely incapable of getting even Itachi to realize he's there. He is also incapable of sleeping, and has to experience every thought and every bit of sensory input that Itachi does. The author admits that writing a chapter sometimes makes her head hurt as much as the readers'.
One can almost pity Madara in A Growing Affection. Hinata's Singularity Rasangan atomizes him, and according to the description seems to slow down time like a real black hole. Due to his immortality being tied to his eyes, he doesn't die until they are consumed. And fittingly, he tries to scream in pain but the sound cannot escape.
A Crown Of Stars: Don Barceló’s fate, a blood-thirsty tyrant that ruled Buenos Aires. Psychic soldiers put him into a mental loop where he relived every torture, rape and murder he had ever committed - including sensory feeds- from the victim’s point of view. And there were hundreds of victims! A medical clip also prevented him from passing out and dehydrating. It was agreed leave him like that for a while and then hanging him.
The Second Try: Gendo's fate. He falls into a coma. Later he becomes kind of aware, but his whole body is completely paralyzed and he can't communicate with anybody. He wonders if this is his punishment, since he can't even kill himself to try and see Yui again.
It happens to Young Link in Link's New Look: Playing Princess where due to Peach's "special" perfume he was forced to act like a girly princess while he was unable to do anything about it.
A similar fate happens to Ben Tennyson in Ben's New Look: Mallrats where due to Gwen's Feminisa poseon spell he was forced to act like a girly girl in a crowded mall while he can't do anything about it.
It also happened to every boy except ironically Naruto himself in Naruto's New Look due to the caged bird seal used by Shizune.
General Marius, a racist, child-molesting (two of his victims were his daughter and nephew) turian was subjected to a similar fate but in his case, it was much faster. Garrus's dad, Avitus, poisoned him with a drug that left him paralyzed but still fully aware his surrounding, then the Papa Woft ripped Marius's heart out of his body while he was in that state.
Tali in the Bad Future, meanwhile, was forced by Gaius to see him killed her daughter, then he tied her to a pillar with her own guts, keeping her alive with nanomachines to make her watching him destroyed Rannoch and pushed the whole Quarian race to extinction.
Makerm was sealed away by his wife to prevent him from massacring everyone outside the North. Just like all examples above, he still has full awareness. Unfortunately, because of that, he constantly tried to process his descendants to escape, leading to Garrus's grandfather's death before the series's start.
Song of the Phoenix. The souls of certain victims of Jusenkyo —the ones who originally drowned in the springs to create the curses in the first place— are trapped in the waters. Some of them "sleep" in blissful oblivion... others exist in absolute, endless darkness as nothing but thinking souls, for however many thousands of years it takes for someone to fall in the spring and, if they're exceedingly lucky, hitch a ride in their body. They can only watch from within the body, unable to interact, until the cursed person dies and the other soul is allowed to manifest briefly. And then they go right back into the spring, and the darkness... It is explicitly stated that the soul of the Drowned Girl from the spring that cursed Ranma went through this for 1500 years, to the other characters' horror.
Praying in Vain: Over the course of the story the protagonist finds and frees the victim/s and the murderer/s of several killings throughout the town's history, trapped in its Dark Worldever since they were killed and continually experiencing their moment of death (including but not limited to bleeding to death, dismemberment and immolation). It's heavily implied that every single person killed there is in a similar state, forever tortured to sustain the town's Genius Loci and at the end, though pissed at the loss of its food, the personification of the aforementioned loci assures the protagonist that she has accomplished nothing, and that there is plenty more where they came from.
If you're a woman in the Emirate of Mecca, the Muslims turn you into a living broodmother and force you to constantly give birth after being raped by impregnation machines - and make you nearly immortal so you won't die in childbirth.
Tails ends up in this fate during the final battle. Dark Tails possessed him and rapidly mutates his body, causing his limbs and body parts to start rotting off. Then they begin to regrow and fall off again and again and again. And for bonus points his jaw falls off, leaving him unable to even scream. Thankfully, Cosmo gives him a Mercy Kill.
Interestingly, this trope could describe Maledict himself; he's a Humanoid Abomination trapped in a decaying physical body for the past five hundred trillion years, slowly watching his empire and the universe come to ruin - and if he dies, it'll spell the end of everything he's worked for.
The fate of anyone who is subject to Forceless possession in Paranormalities. Not only do Forceless completely hijack the host's body and physically shape (read: mutilate) it to their desire, the victim is consciously aware of what is happening to him/her and only those with Force Sensitivity can tell of their predicament. Death is a mercy for those who have been possessed (especially for Dynn Manthis). So far, the only exceptions to this rule are those who willingly serve the Forceless Collective, Maesterus and Zolph Vaelor. Maesterus and Zolph are part of the same bloodline, and the immunity has strengthened every generation. Maesterus was still mutated by the Forceless symbiote, but he eventually became immune to the body-jacking, while Zolph was always immune to possession altogether, thus making him the number one threat to the Collective.
In Part 2 of Clash of the Elements, this is Cackletta's final fate, in which her 'Second Life' spell in combination with Alpha's nanomachines will leave her in a perpetual state of life and death until the spell runs out.
TRONFanon holds that rectification is like this, the poor Program intermittently conscious and aware of the horrible things s/he is doing to serve their "masters," but unable to stop themselves from carrying it out.
Early in a Werewolf: The Apocalypse fan fic, the main character suffers sleep paralysis in his bathtub and wakes up right before drowning. As if that wasn't horrifying enough, the character is later kidnapped by the villains and forcefully possessed by an evil spirit. He likens it to the episode he suffered earlier, except he actually drowns.
In Yu-Gi-Oh The Thousand Year Door, Redux, the Shadow Queen spent the first few three centuries of so of her millennium-long imprisonment like this; she was manacled tightly in a very small, dark cell, unable to move a muscle, fully awake and aware. For much of the fic, the readers - and the protagonists - are led to believe that the Three Heroes mercilessly sentenced her to this fate, and never intended to release her. The truth comes out much later. The same magic that made her a prisoner was supposed to administer therapy to nurture her mind so that hopefully, once all her crimes were forgotten over ten centuries, she could be released after accepting redemption. She was even offered a chance to sleep through it. She rejected both, and fought to free herself of the chains until she succeeded, and then spend centuries plotting revenge.