Panzer World Galient: Queen Felia -The Hero's mother- was captured by the Big Bad, frozen alive, framed and set in Marder's private chambers to adorne them like a strange blend of living painting and statue. She is aware, but she can't move, talk or even blink.
At the start of Yes! Precure 5, Nuts was trapped inside the then-unopenable Dream Collet.
Queen Beryl doomed Jadeite to "eternal restless sleep" in Sailor Moonafter his repeated failures. Which meant trapping him in a giant crystal and sealing him away somewhere. It's a very popular starting point for Fan Fiction. And lest you think this is an example of Never Say "Die", Beryl had no qualms with outright killing her failed henchman, leaving this punishment as particularly gruesome in retrospect.
Hidan's fate in Naruto. He gets blown into pieces, and buried in a hole... but he's immortal, and his severed head continues to curse Shikamaru right until he's covered over while rotting slowly away from the lack of nourishment. According to the second fanbook he is going to die eventually.
Itachi traps Orochimaru into a previously thought to be inescapable genjutsu that was meant to go on for eternity. Takes a few hundred chapters, but Orochimaru eventually gets out. Itachi later traps Nagato in the same genjutsu after both of them are revived by Kabuto.
This was revealed to happen to those brought back by Kabuto's Edo Tensei spell who are under direct control of Kabuto.
Quite fittingly this is also Kabuto's fate, forced to repeat an endless "Groundhog Day" Loop within Itachi's genjutsu for eternity...or at least until he admits his mistakes and tries to achieve greatness on his own and stop copying other people.
This is also the case for every sealed Bijuu.
During Naruto 5: Blood Prison, Muku (The son of the Big Bad, Mui ) was trapped in the Box of Ultimate Bliss for ten years after attempting to open it for his Village. The first thing he does is to stab his dad in the chest, and morphs into Satori, going on a destructive rampage. The fact that the Box was indestructible from the inside didn't help. But was eventually freed when he incinerated himself.
Kakurenbo—While we cannot be sure how aware they are, the children captured by the demons are used as living batteries, like The Matrix but without the potentially cheerful virtual reality. It gets worse at the very end, as the numbers of child-batteries are revealed, each hooked up with a light above them. And then we see a little boy, whose light flickers, and then goes out.
The "winner" of the game is possessed by the demon fox and lures the next group of children. Made worse by the fact that the fox goes from possessing a young girl to taking over the brother who came only to save her.
Episode two of Vampire Princess Miyu, "At The Next Station". This is the fate of the women who fall prey to the temptation of the Shinma Rho-Ah, and take him up on his offer of enhanced beauty... only to end up frozen in time, like beautiful mannequins dressed in expensive clothes, never to age or decay... at the end, even the one who got decapitated during the battle between Rho-Ah and Miyu is still alive, just like the rest of them — whimpering and sobbing quietly through paralyzed lips.
In the second OAV, it's downright stated that Ranka's victims end up in a similar state, transformed into bare and listless mannequins that she keeps into her school's warehouse. She even uses one of them as a shield during her fight with Miyu, and Miyu is horrified when Larva accidentally hits the doll with his Razor Floss and not only it emits a whimper of pain, but it bleeds. This is lampshaded earlier, in this conversation that takes place during Ranka and Miyu's first encounter:
Ranka: (pets her newest doll, erm, victim): No longer will you age or grow decrepit. You can live forever, looking the way you do now...
Miyu: (steps in) And thus... will the life energy that you emit become my sustenance...!
Ninja Scroll: The immortal, regenerating bad guy gets encased in molten gold, gold which he had schemed and murdered to claim, no less, and sank to the bottom of a lake.
This was a punishment dealt to Team Rocket (temporarily, thanks to a between-episodes Reset Button) in an early episode of Pokémon.
Sabrina's dolls. While they couldn't move or actually talk, it was pretty clear they were conscious. Good thing Ash found a way to beat her.
In the Pokémon Special manga's FRLG arc, Silver gets turned into stone along with four other Dex Holders and he alone stays conscious throughout the series until he gets unfrozen along with the rest of them.
A relatively early episode of Diamond and Pearl featured the cast searching for a Sandshrew that was trapped in its Poké Ball, inside a locker at the bottom of a flooded town. Pokémon are completely aware of the outside world while in their balls.
Art teacher Hitomi Ishigami enjoys doing this to her students in the Rosario + Vampire manga, for the sake of "true art". She picks out girls to be her "models", then Takes Them For Granite and lets them cry as much as they want (their tears stream down their stone faces to get this across).
In Bleach, the end of the fight between Mayuri Kurotsuchi and the Espada Szayel Aporro Granz. Due to implanting an egg of himself into Nemu to resurrect himself, Szayel ingests a massive dose of a drug that grants superhuman senses, speeding up his perception of time. With seconds seemingly taking centuries for him, and his body unable to keep up, he is utterly incapacitated. Kurotsuchi then stabs him through the hand and chest, not quite piercing his heart. While in real time he died only a couple seconds after the drug took effect, to him it felt like being stuck in place for several hundred years.
The comic in UNMASKED reveals that Ulquiorra was unable to hear, speak, smell, feel, eat, or sleep due to his mask covering everything but his eyes. He was able to move, but since he lived in Hueco Mundo, it didn't matter where he went; each pile of sand was exactly like the one before it.
The Vandenreich Emperor Yhwach was born blind, deaf, mute, and paralyzed. However, by transplanting portions of his soul into others and then absorbing their souls when they die, he was able to cure himself. He must constantly absorb souls or else he will revert to his previous state.
In YuYu Hakusho, Kurama traps Elder Toguro in a plant that drains the energy of its victims until they die, while showing them a hallucination of their worst fear... but since the latter can't die, he's stuck seeing his worst fears for eternity.
Mukuro's father met a similar fate thanks to a conjoined effort by Kurama and Hiei, the latter of which donated him to Mukuro as a gift. The parasitic plant binds him completely, but also sustains him so long as his head remains intact. So, all he has to do to get out of it is convince her to break his skull open... good luck with that.
In Part 2, Big Bad Cars ends up gaining immortality and an auto-evolution ability after combining the Stone Mask and Red Stone of Asia. Joseph uses this ability against him by throwing him into an active volcano, and with some luck manages to make it erupt with enough strength to launch him to space, where he's unable to return to Earth. Unable to die even though he wishes for it, eventually his mind shuts down completely.
Part 4 has Josuke inflict this punishment to multiple villains, because he refuses to kill anyone. He fuses Angelo to a rock (and for kicks, puts up a sign saying "Please leave your Dog Crap here" which Angelo HATES), and he also fuses Miyamoto into a book (it's said that the book became a notable icon of the town, and people can sometimes hear whispers coming from it...). A variant happens with Akira's Stand Red Hot Chili Peppers, which gets trapped inside a tire and hurled into the sea. Akira does not die, so it can be assumed that Red Hot Chili Peppers is stuck like that.
In Part 5, the Boss Diavolo/King Crimson was struck by Giorno's Arrow-struck Stand, Gold Experience Requiem, which sent him in a mental, eternal loop of deaths, while his body stayed idle, seemingly comatose.
In Part 7, Magenta Magenta's power gives him perfect defense, including not needing to breathe, as long as he stays still. The heroes wrap him in wires and throw him into a river, where he sinks to the bottom. He activates his power to keep from drowning, but can't free himself, so he opts to wait underwater until his ally comes to rescue him. His ally never shows, and he suffers a similar fate to Cars, complete with a similar narration.
The water of the Delaware kept up its constant rhythm as it flowed past the river bottom... and as time passed, Magenta Magenta...
And stopped thinking.
In the classic Nickelodeon anime The Noozles, the soul of Sandy's grandfather is doomed to spend the rest of eternity trapped inside a crystalline orb in another dimension.
Used for a Karmic Death in Franken Fran. An old, rich woman was seeking to have her youth restored, and had her servants murder any doctor that couldn't come up with a permanent answer. She's also had herself mass-cloned, only to murder her clones one by one and drink a solution made from their eggs, one of the partially-successful treatments. She hires Fran, who comes up with a treatment that seems to have results... then has her men cut Fran's head off afterwards. Unfortunately for the old woman, Fran is an Artificial Human, capable of stitching her own head back into place. She confronts the old woman afterwards, and notes an unusual rash on her arm... Turns out, as aging is caused by programmed cell death, Fran had adjusted the woman's cells to be the one type of cell that is not pre-programmed to die... cancer cells. As she says it, the old woman collapses into a giant pile of cancerous cells. And then Fran tells her that, theoretically, she'll now live forever.
Most of Fran's patients wind up in this boat, really.
The Mazoku from Slayers have Raugnut Rushauvna (or however you spell that), a very, very nasty curse that makes its victim completely immortal... while also turning their body inside out and causing it to continually devour itself and regenerate, over and over and over again, for all eternity.
Angel Sanctuary has a doubly terrifying version revealed towards the end. The most powerful angel, Adam Kadamon, said to be mother/father of all angels, was imprisoned for probably thousands of years by God because he was afraid of its power and was slowly taken apart to be fed to its children the angels. Yes, you got it right, the cute little angels are fed their mom/dad; no wonder most of them are not so pure. By the events of the books only a deformed head is left which is still conscious and able to talk, but gets finally released by the good guys.
Gundam also uses it on occasions. Zeta Gundam might give the idea of Kamille being thrown into one of those (though probably only lifelong) situation at the end, but he gets better in the sequel, Gundam ZZ. Villains like Katejina from Victory Gundam or Shagia Frost from Gundam X end up at least in one way or the other crippled (Katejina is blinded and amnesiac, Shagia is wheelchair-bound — Gundam's not that far into mysticism, so no punishment beyond life so far). Though, Gundam X has Lucille Lilliant a.k.a. Lorelei (a good minor character) being put in a forced coma and locked in a capsule for 15 years or so, mostly cut off from the real world. She manages to contact her ex-pupil Jamil through the body of a fellow Newtype, Jamil's protegée Tiffa, and is saved.)
Anyone who is infected with DG Cells in G Gundam. You either become a zombie used to power the Dark Army, or slowly go insane/rabid.
The manga Blood Alone has a killer who can jump to other bodies when he dies. Unfortunately, the last people he fights are a vampire and rather savvy human. She turns him; and then he breaks his neck just as he turns into a vampire. The killer is now frozen in the body of an permanently broken necked vampire. They lock him up in a room in the basement of a hospital.
The manga Tokyo Crazy Paradise has a scene in which exhibits on display in cabinets turn out to be human beings, posed like famous works of art. The cabinets contain machinery that keeps their occupants alive and immobile. They are intended for sale to rich collectors who are perfectly aware that the exhibits are alive and helpless, and quite happy to leave them that way. The heroine Tsukasa attempts to free them, but is caught and ends up frozen in a cabinet herself. Fortunately for all of them, the auction is raided and the exhibits are set free.
In one scene in the Elfen Lied manga, there's a diclonius who is not much more than a head and a chest within a completely enclosed metal box. The head is covered by the same helmet and mask as the dicloni in the lab. The diclonius' only purpose is to use its telepathic abilities to sense others of its kind and serves as a biological detector device.
Not only that, but a device is connected to the girl's spine to make her experience continuous pain in order to prevent her from lashing out at her tormentors.
He also stated that after raping her (before cutting her in half), he cut out her vocal cords. This series doesn't have enough generosity to its characters to do it in a clean way, so you must use your imaginations on how that went.
Because that isn't enough, her psychic projection of herself is nothing but a scarred upper-body with a faceless, missphapen head uttering only "It hurts", "Kill me" and "Run" over and over.
Greed found himself in this situation in the first Fullmetal Alchemist anime, sealed in a skull stuck in a wall for hundreds of years. He chose death in favor of letting it happen to him again.
In the manga/second anime, this happens to any poor soul who's put into a Philosopher's Stone to be used as an alchemy amplifier. The victims can scream, but because there is no one to get them out of there, they are always screaming, with no plausible hope of ever getting out of the stone other than being used to fuel an alchemic transmutation, wherein they effectively die. On the plus side, Van Hohenheim, who in essence is a walking Philosopher's Stone, took the time over the many centuries he was alive to talk to and calm down every single soul inside him.
Also, at the very end of the climax, Father is dragged back into the Gate of Truth, screaming in abject horror before it shuts, locking him away in a hell he had desperately tried to evade.
In Nightmare Inspector, while Hiruko was still Chitose Kurosu, his masters broke all of his limbs. All he could do was scream.
Yu-Gi-Oh! has this. Characters frequently get their souls taken from them and imprisoned in cards or in the Shadow Realm. No idea what they can feel while they're inside either one.
According to the Word of God, Yami was aware of time passing when he was sealed in the puzzle for three thousand years. There's a reason he was not entirely sane when he first awakened.
Demonstrated quite nicely in Season Zero; he had a tendency of inflicting punishments like this to those who cheated in his...games. And there are very few who didn't cheat.
The Shikon no Tama is formed through a miko and a combination of youkai being locked in a battle. The souls of the youkai and Midoriko still battle endlessly inside the jewel, for the 500 years or so of its existence. Near the end of the series, The Shikon no Tama tells Kagome that she was born to keep the battle inside the jewel going on, that she was born to be trapped inside the jewel and battle inside it forever, that there is no right wish to make, and that it can't ever be destroyed. Thank god that's not exactly true.
Kagome ends up going through this herself in the first movie. To clarify, she's brainwashed by the Big Bad and forced to attack Inuyasha with the intent to kill. Throughout the entire experience, Kagome is fully conscious of what she's doing and unable to control her own body.
Several truly chilling instances in Mouryou No Hako, the most awful being the fate of Yuzuki Kanako. She would have been better off had she died the night she was run over by that train. Instead of that happening, however, her mother/sister took her to an experimental 'hospital', where her ex-Unit 731 dad/grandpa proceeded to cut off all four of her shattered limbs and keep her hooked up to a warehouse-sized room full of life support machines. Then she's stuffed into a box by a man who loves her, and dies one hour later. All while being aware and awake.
There's also Kubo Shunkou, the disturbed perpetrator of the severed-limb murders. Almost religiously obsessed with boxes and closed spaces since childhood, he ends up offering himself to Kanako's dad/grandpa as another guinea pig. When Mimasaka and Youko decide to escape with him (now nothing more than an upper torso and head) in a box, he somehow escapes from the box and kills Mimasaka by chewing his neck. Kubo seemed happier in the box than outside of it. He was still insane, though.
What happened to Kate's father in Love Is In The Bag, specifically being stuck as a portrait of himself for fifteen years. And it's implied that it'll happen to Kate as well.
What happened to Kaoru in an early mini-arc in Rurouni Kenshin, thanks to Kurogasa. An extremely Ax-Crazy swordsman and hypnotist who wants to fight male lead Kenshin and kidnaps her to force him to, as soon as Kenshin reaches for them Kurogasa hypnotizes the poor girl into complete paralysis. This means, not only she can't move her limbs or talk... but is slowly, painfully and inexorably asphixiating, since her whole respiratory system is under paralysis too. And she's fully conscious, helplessly watching how Kurogasa and Kenshin fight it out and Kenshin is reverting to his Knight Templar Battousai side only to save her, since the only way to break that "spell" is to kill Kurogasa himself before she kicks it... There's another way, though: to have Kaoru overpowering the hypnosis with a strong will to live. And she does it in the nick of time. Kurogasa still committed suicide in the end.
Griffith from Berserk suffers a purely physical, non-supernatural version of this: after sleeping with Princess Charlotte out of grief, he is imprisoned by the Midland King and tortured for a year. By the time Guts, Casca and the other come to rescue him, he's horribly emaciated; his tendons have been severed, preventing him from holding a sword or even standing up right; and his tongue has been cut out. All the while he was conscious of it, and speculates whether or not he's still sane... all of this pushes him to both the Despair and Moral Event Horizons to escape from it.
In Mermaid Saga, it's unclear whether Akiko from "Mermaid's Gaze" died or was left petrified and conscious for a hundred years. All that we do know is that her eyes still work. Mana claims that Akiko was dead all along, but it's clear she's just trying to make Yuta feel better.
Piedmon suffers this fate near the end of Digimon Adventure, when he's thrown into MagnaAngemon's Gate of Destiny, which according to Word of God leads to a pocket dimension from which there's no escape. And since Digimon are functionally immortal, barring being killed by someone else... this was a well-earned KarmicFate Worse than Death.
In Bakugan, this was intended to be the fate of Emperor Barodius by Code Eve, the god of the Bakugan, as punishment for attempting to destroy a peaceful planet in persuit of power. And she was quite thorough about it. She imprisoned him in armor crafted from his own evil, sealed him in another universe, and left him tied to his throne for all eternity with only his own madness and his equally insane guardian Bakugan to keep him company. By the time we actually see him again, he's gone completely insane, declared his old self dead, and invented a new persona for himself called Mag Mel. Unfortunately, he had a Psychic Link to Dan that let him absorb Chaos Energy to escape, but if it weren't for that it'd be a rather karmic end.
Bakugan sent to the doom dimension suffer from this. The place is so inhospitable that they are forced into a dormant state where all they can do is think about how much they hate their situation, except for Reaper who stays conscious but gets hideously wounded.
In Shaman King, Yomi's Hole is a cave where you lose all senses: you can't see or hear anything, and you enter some kind of existential panic; we actually see what it's like when Ryu enters it for just a minute. It has been mentioned that many young shamans wanting to enhance their furyoku lost their sense of direction inside and stayed the rest of their lives in there.
Baccano! has a lot of immortal characters, and a couple of them end up like this. Perhaps the most clear-cut case is Dallas Genoard, who really annoyed the Gandor mafia family, overconfidently assuming that since he could regenerate from any wound, they couldn't hurt him. So they did what the mafia does best and gave him Cement Shoes, leaving him to eternally drown at the bottom of the Hudson River until he either got dredged up or died of old agenote Most immortals in the series had Complete Immortality, but he only had From a Single Cell regeneration so he still aged and would die from it.
In Mahou Sensei Negima!, this is the final fate of nearly all of the puppets of the Lifemaker. Being annoyingly hard to keep dead and protected by several layers of barriers, Evangeline devised a spell that completely froze their surroundings instead, keeping them trapped yet conscious for all eternity.
Near the end of Utawarerumono, the main characters enter a partially-technological dungeon and find it infested with standard-issue Slimes, which they soon get bogged down fighting - swords and arrows don't seem to do much to impede them, but on the other hand, they don't seem able to do much to harm the heroes, either. In the next episode, however, it turns out that those blobs of reddish goo are actually the previous occupants of that 'dungeon' - actually an underground laboratory from Before The End, and that they were transformed by the titular demon-god as punishment for dissecting his lover in an effort to find a way to strengthen their bodies so that they can return to the by-then poisonous surface. So, in the true spirit of an Utterly Pissed-Off Genie, he decides to fulfill their wish for a 'body that will never die'. And they've been there ever since. For what must be several thousand years by the time the story takes place. They deserved it, but still...
In Heaven's Lost Property, Chaos is defeated the first time when Ikaros sends her to the bottom of the ocean. Chaos is immortal, but the water pressure is so great that she's pinned. She eventually escapes.
In the first Dragon Ball Z movie, Prince Garlic Jr. Wishes for immortality which he gains, he then attempts to try and trap Goku in a dimension called "The Dead Zone" which is averted by Gohan pushing Garlic Jr. into his own trap. It's bad enough being trapped in a place called "The Dead Zone" but it's even worse when you're immortal thus trapped for all eternity, though in the main series he escaped only to be trapped yet again though when he returned he didn't seem traumatized, he actually looked rather smug, meaning it probably wasn't that bad as the name implies.
Fridge logic applies, though, since earlier in that same fight Buu pulled a shake and a magazine out of thin air to taunt Gotenks by looking bored. If he can create ice cream and reading material from nothing, why does he care if he's trapped in the Ro Sa T alone or if he gets out, since he's just going to destroy everything outside and be alone anyway?
Yuki in the Endless Eight arc of the Haruhi Suzumiya series is forced to relive the same two weeks over and over again for nearly 600 years. And while she's the only one of the SOS Brigade to remember it all (while the others just get an odd sense of deja vu,) she's unable to do anything about it because her orders forbid her from directly interfering.
In One Piece, this is the fate of anyone who loses in the Colosseum of Dressrosa. They are dumped into a pit and turned into toys that, while they maintain their memories, are unable to do anything but the bidding of the Don Quixote Family and are, for the most part, unable to say anything about it. Also, almost everyone else the toy-people ever met forget the toys ever existed as humans.
In Life Is Money, the characters play "The Nightmare Game," in which they must roll a die every day to determine which of their senses will be restricted. Depending on their roll, they will either be blindfolded, nose-plugged, forced to wear soundproof headphones, gagged, or paralyzed from the neck down.note The sixth possible outcome, "Spirit," removes all current afflictions. The rolls are accumulative; a player may have all five restrictions at once. Additionally, a player dies whenever they suffer a Despair Event Horizon, and being alone in one's mind is considered one of the worst ways to reach this.
In Ajin, The treatment of Ajin at the hands of human "researchers" is this with a heavy dose of Nightmare Fuel. Blindfolded, Vocal cords removed and strapped down on a table while various experiments are performed but all the experiments end in death. A fair amount of the experiments are simply done to see how much pain the Ajin can take. Once the Ajin die they wake up back on the experiment table whole and ready to start the whole process over. The Ajin are immortal and near as anyone can find they cannot die.
In Attack on Titan, the true nature of the Titans is revealed to be this. They were all once humans who were somehow transformed into Titans a century earlier. Unable to control their new forms, they're only driven by their basic instincts to feed. With at least some form of awareness left. Many of the characters are understandably horrified by of the implications of this discovery. What's worse is that it's not even clear how it occurs, but that it could happen to anyone. As Connie found out the hard way.