Though if you think that's bad then just wait until you hear what happened to Blurr. He was crushed into a cube by Shockwave and was confirmed to still be alive, then he was supposedly put into an incinerator soon after though there is some debate amongst the fandom about this.
Although one of the comics shows Cliffjumper carrying the cube around with him, so he aparently saved from that last bit. Unfortunately, Cliffjumper doesn't seem like he knows how to get Blurr back to his old self...
In an episode of the Legion Of Superheroes, the wizard Mordru is wrapped in a metal cocoon and sunken to the middle of the planet. Pretty harsh when you consider his eyes were still moving as he was buried, and the planet probably has a molten core... so either he is buried alive or melted. Pretty harsh for a team that works with the police and United Planets.
A man with an intangibility device finds the effect spreads to his body without the device being engaged. In the end, his Power Incontinence winds up causing him to phase through Batman's hands, through the floor, and into the Earth. The best case scenario is that the lack of Required Secondary Powers will mean incineration by the mantle, or death by suffocation, starvation, dehydration, or at least old age. If not, he's permanently phased into the core of the earth. Forever.
Another villain, Inque, can shapeshift by turning into liquid and reforming. A guard at her prison who had a crush on her is sweet-talked into helping her, but wants powers like hers in exchange. She gives him an incomplete version of the formula, leaving him an immobile half-liquid blob. His guard is seen talking to him just as he once did with Inque, hinting that history may repeat itself, but that's unrealistic: he can't move, and doesn't know enough about the formula to instruct her on how to fully Inque-ify him were she to agree.
Earthmover had fused with Earth itself, for years. His episode centered on his anger at his unjust fate and wanting to see his daughter again. Thankfully, it gets better for him, since he found a way to control the Earth itself, then found release when he was finally killed in a cave-in.
In Superman: The Animated Series, this happened to Metallo at the end of “Action Figures” (temporarily; he gets lucky and is rescued by a criminal organization). He angrily describes it to Superman in the next episode where he appears, “Heavy Metal”, (the experience obviously having driven him insane and sending him on a Roaring Rampage of Revenge):
Metallo: Do you remember how you left me Superman? Buried in rock? I couldn’t move! I couldn’t see! I couldn’t hear! But I could think. And all I thought about how I was going to make you pay!
Justice League Unlimited is usually nicer to its villains than Batman Beyond, but makes an exception for Mordred: Morgaine Le Fay's spell gave him eternal youth and life, but he's stuck as a child. When tricked into making himself an adult (thus causing him to disappear, as he'd cast a spell that teleported all adults to another dimension) it turns out that by breaking the youth spell, "all he has is eternal life." He's 1500 or so years old and counting, showing every bit of it, and is now essentially immobile in a chair at his (still-youthful) mother's home. And it's only going to get worse.
At the end of the two-parter "The Once And Future Thing", Chronos winds up permanently trapped in a timeloop, being forever berated by his shrewish wife. At first glance, Chronos does not appear to be aware of his fate, but if you look closely when Chronos presses the button on his belt, you can see that between screen-flashes there is a one-frame image of Chronos with a look of horror on his face.
In most adaptations, the Joker's signature venom kills people. However, in the first episode of The Batman, what it does to one poor orderly at Arkham is worse, as Alfred tells Batman when asked about the man's condition:
Alfred: Aside from the ghastly grimace, [he's] fit as a fiddle. The poor soul simply seems to be a prisoner in his own body.
Fortunately, Batman is able to find a cure by the end - this time.
The famous "Roswell That Ends Well" episode of Futurama had Bender's fall off of the back of the Planet Express ship as it was returning to the present, causing his head, which holds the AI, to be buried under the New Mexican ground for 1,000 years until the crew picked him up. To him, however, it was pretty good until the crew showed up.
The episode "A Head in the Polls" begins with the collapse of a titanium mine, trapping all the robot workers inside (some of whom are seen pinned in the entrance, still twitching). The proposed rescue plan is to "pave over the area and get on with our lives."
Robots in the Futurama world seem to be programmed to not be bothered by this sort of thing. Besides the "Roswell That Ends Well" example, in the "Bender's Big Score" movie Bender is perfectly happy to spend a total of millions, maybe billions of years hiding in a cavern with only his own time duplicates for company. A "what if" episode also had him buried underground for 500 million years and coming out completely unaffected.
It could also be that Bender's intense narcissism enables him to spend however long he needs spending quality time with only Bender for company.
This was later subverted when it's discovered that a time duplicate of Fry goes back in time and gives Seymour much love and attention. (Way to spoil the sad ending, Groening)
Lampshaded in the episode "Raging Bender" when George Foreman says, "As a head without a body, I envy the dead." (Oddly enough, most of the celebrities who have ended up like this have no problem with it.)
In the Sonic Sat AM Saturday morning cartoon (as well as Sonic Underground, and the Archie comics), roboticizing a person meant turning them into a machine, eliminating their free will. However, their minds still function, causing them to be used as slaves to Robotnik, knowing what's happening but incapable of doing anything about it.
In Thomas the Tank Engine, Duke relates the story of a misbehaving engine who was turned into a generator, with his face still intact and presumably still conscious. It gets even more horrifying when the Fridge Logic sets in that he was likely buried along with the rest of the old railway and might still be down there underneath several feet of dirt.
Duke himself was abandoned in his shed, which was covered over by nature and buried for many years, until he was unearthed in "Sleeping Beauty".
Since from what we've seen when the fires in one of the engines are dropped the engine goes to sleep. So the engine in Duke's story probably is not conscious, but is more likely in a coma-like state. Not completely averted, though, because they can still dream in that state. In fact, one of the specials had a scene where the engines were dreaming about what might happen if the railway didn't get enough visitors to stay in good financial shape. Gordon dreamed that he was turned into playground equipment, James a circus game, Edward a scarecrow, and Percy a roller coaster.
In the special Misty Island Rescue, Thomas and the three Logging Locos get trapped in an underwater tunnel (Bash, Dash and Ferdinand running out of fuel) with nobody knowing where they are.
The ending of the Silly Symphonies short Peculiar Penguins, ends with the shark, who was chasing the protagonists for half the picture, with a very large rock falling into his belly, trapping him at the bottom of the ocean to possibly starve to death.
Wild Kratts has Donita Donata who specializes in "living jewelry", i.e. living animals frozen in suspended animation and attached to horrendous fashion. And yep, they're still conscious.
Paradox in Ben 10: Alien Force found himself trapped in the event horizon of his time tunnel for hundreds of thousands of years, unable to escape or die.
In an episode of Darkwing Duck, "U.F.Foe", Darkwing finds his brain taken out by aliens and his body controlled by remote. Although he has no mouth (or beak) and we "hear" his screaming thoughts, amazingly he can still kick ass as he destroys the computer brain and saves Launchpad from the same fate!
Similarly, in an episode of DuckTales, the Beagle Boys manage to take control of Gizmoduck's armor by remote - while Fenton is still wearing it. He's not at all happy with being forced to rob his own employer in broad daylight... or stealing his crush's car, for that matter.
The Chronicles of Riddick: Dark Fury has the eponymous hero go up against a madwoman who "collects" criminals and keeps them awake but practically frozen in artistic poses as part of a grotesque, living gallery. She created a type of stasis that slows their bodies down to a crawl but lets their minds be fully functional. It takes them a day and some excruciating pain to even blink their eyes.
In The Fairly Oddparents, it is eventually revealed that everything a child wishes for are put into "storage" in giant lockers. This includes any wishes that result in sentient creatures. And since they are immortal, they are stuck in a small, dark area forever. The fact that no one bats an eye at this says something.
Timmy's undone wishes are even worse, given that they had to abandon the locker concept entirely and port them all to an island (possibly a commentary on his tendency to hit the Reset Button every episode). It's revealed that the leader of this island is Timmy's imaginary friend Gary, who also fit this trope in his first appearance. After Timmy got Cosmo and Wanda as his fairy godparents, he forgot about his friend... but Gary never forgot about him, and was trapped inside Timmy's imagination, fully aware that he was being ignored. It's no surprise that he went for the revenge route.
The fate of Turbo Thunder's parents in Wishology. Luckily, Timmy saves everybody in the end, including them.
"Paralytic fluid" in the Ćon Flux episode "Ether Drift Theory". The Habitat laboratory is submerged in a lake of said fluid, which paralyzes those who fall in it, with no hope of rescue. But they are still conscious. This happens to Aeon herself at the end of the episode. The last scene of the episode is of Aeon, paralyzed in the fluid, as the two halves of the item that would neutralize the solution slowly float in front of her eyes, collide, and go in different directions.
In The Venture Bros. episode "Return to Spider Skull Island", Doctor Orpheus deals with two Jerkass rednecks by trapping their souls in a Homeboys figurine. They can actually be heard screaming.
A version of this happens in Robot Chicken where a werewolf is reduced to a bloody pulp by More Dakka, cremated, had its ashes snorted and later crapped out and roasted in the sewage treatment. This is then shown to be a Tabletop RPG, where the Game Master states that it's technically still alive because the bullets weren't silver.
The Secret Saturdays: In one episode, the family face against a warrior king whose thirst for power long ago could not be quenched. Seeking to use the Methuselah tree, which makes all the water on Earth, he ended up entombed in salt due to the tree protectors (giant insect-like crab cryptids) causing an earthquake. Years later he breaks out of his imprisonment when the salt crystal gets exposed to water. Anything that he touches with his right hand turns or gets encased in an unbreakable layer of salt, which he uses to almost accidently turn the tree itself into salt. In the end its revealed his thirst for power has now became a literal, unquenchable thirst, yet unable to touch water to quench it. He demands Zak retrieve the sap from the tree to finally end his suffering. Later he uses a flower from the tree to finally quench his thirst. As it turns out, he became nothing but living salt and drinking the sap from the flower reduced him to a pile of salt, finally ending his suffering.
In Trollz, Zirconia was turned into a tree for 3,000 years. It's a bit more complicated than that, though; at first, she was simply imprisoned within the tree. As time passed, she became part of it. She was conscious the entire time.
Spinell, her husband, was trapped in the form of a dragon. That couldn't talk.
The short film Alma is about a little girl lured into a sinister toy shop by a doll that looks just like her, ending with her becoming the doll after touching it and the shop setting out another doll to lure another victim.
In Gargoyles, the Gargoyles whose bodies composed the Cyborg Coldstone are given a moment of freedom by a spell that allows them to possess the bodies of their living brethren in the clan. Coldstone and his mate briefly contemplate keeping the bodies, but eventually give them back up shortly after it's discovered that the Gargoyles they're possessing are still conscious in their bodies. Fortunately, this was part of Puck and Xanatos' plan to transfer two of their consciousness' into new android bodies, leaving Coldstone in sole control of his own.
In the backstory to My Little Pony: Friendship Is Magic, Nightmare Moon was imprisoned in the moon for a thousand years, and it's implied she was aware the entire time. However, her sanity doesn't seem to have suffered from the experience.
There have been fanfics written that try to describe what her isolation must have been like, especially considering that the reason she turned evil in the first place was because she was lonely. Some of these fics imply that Celestia offered her an early release if she reformed; others aren't so generous.
A later episode confirms Discord, when encased in stone, is able to observe the world around him, which is probably why he was placed in the middle of an empty garden where nothing important happens.
There is also the Windigos, spirits of cold and hatred that feed on hatred. They cause ponies to hate each other and then freeze them alive so they'll have a continuous food source.
King Sombra of season 3, trapped in a glacier for 1000 years while he also cut his kingdom off from the outside world for that long.
In the original My Little Pony, ponies were at various times turned to glass, turned to stone, and frozen in ice.
In Batman: The Animated Series, Grant Walker, a sociopathic millionaire, has Mr. Freeze build a duplicate cryogenic suit for him and has him undergo the same chemical process that happened to him in order to obtain immortality. At the end of the episode Walker is frozen in an iceberg, sinking towards the bottom of ocean, condemned there for eternity. The last scene shows him watching a fish swim by, then he screams bloody hell.
Well, he was. A comic followed up his story by showing that he managed to get out (cause icebergs do melt ya know?) and tried returning to Gotham to get revenge upon Freeze after finding out that Freeze's condition had destroyed most of his body and the same thing would happen to him eventually. He was captured and imprisoned after Freeze almost killed him.
Poison Ivy, does this to a bunch of rich industrialists she blames for the destruction of the earth's various plant species, and natural habitats. She lures them to a resort and spa, floods their bodies with a biochemical by tricking them into eating food and water, loaded with it, and eventually they turn into human trees. Fortunately Batman is able to save everybody.
After coming back their first experience with the time machine, they bring back a T-Rex which tries to eat Candace only to be hit by Dr. Doofenshmirtz's freeze ray turning it into a living statue. He wanted to use the same ray on Perry the Platypus and other secret agent animals.
The Galaxy Rangers episode "Psychocrypt" demonstrated that after having their soul torn out painfully, those tossed in the device are fully aware of what's happened, their Life Energy is used to make a construct the Queen (the person who put them there) can see and hear through, forced to do her bidding. God Save Us from the Queen!.
Jimmy Two-Shoes: First off, it's implied that the other members of the Heinous family are still conscious in their Human Popsicle state. There's also a throw-away joke about a gnome being completely encased in gold while still conscious.
At the end of the Superman: The Animated Series episode "Action Figures", the android Metallo is left encased in lava underneath a volcano. His Inner Monologue reveals that he is unable to see or hear anything (in addition to the loss of taste, touch, and smell from being a robot in the first place). To keep himself sane, he gives us this chilling thought:
Dark Danny's ultimate fate in the Danny Phantom special "The Ultimate Enemy". He's trapped in a Fenton Thermos and exists outside of time, for all eternity. Hopefully.
In Beast Wars, and thus throughout the rest of the Transformers: Generation 1 continuity, it is revealed that Starscream has a mutant, immortal spark. After being killed by Galvatron (again), Starscream spent countless centuries as a disembodied spark, drifting through the cosmos, before finding a way to go back in time, through the same Transwarp time hole that brought the Maximals and Predaconsof Beast Wars into prehistoric Earth. After being defeated here, his spark was once again doomed to wander the cosmos until it could hopefully possess some being.
Near the end of Monster Truck Mater, Tormentor (Mater's monster truck wrestler alter ego) actually traps Paddy O'Concrete (an Irish modified cement mixer monster truck) in his own cement.
South Park gives us unfortunate kindergarden teacher Mrs. Claridge, who is burned so horrifically in an accident caused by the boys in pre-school that she's confined to a mechanical wheelchair, unable to move or speak, except beeping one time for yes, and two times for no (in a direct Shout-Out to Captain Pike from the Star Trek episode "The Menagerie"). This earns her the sympathy of her fellow civilians, but things really go downhill for her when her chair's batteries go dead.
...in the middle of the street, and the townspeople think she's trying to commit suicide.
One wonders how Teen Titans villain Malchior took being imprisoned in that book for a thousand years. (Well, he does tell Raven he was able to spend the time reading, but then, he was lying to her most of the time.)
Another example of such a fate happens to Ch'rell, the Utrom Shredder, in the 2003 Teenage Mutant Ninja Turtles cartoon. After having battled and defeated him many times in the past only for him to return for a rematch later every time, Splinter and the turtles, despite an interruption by Ch'rell, who beats such stuffing out of them that they spend the next episode recovering from their wounds, successfully destroy his spaceship and, along with him, Karai, and Dr. Chaplin, are transported to the safety of the Utrom homeworld by the Utroms themselves just before the ship explodes. There, everyone is attending as the Utrom council places Ch'rell on trial. The council finds Ch'rell guilty and sentences him to eternal exile to his new home on the ice asteroid belt of Mor Tal, where he does very little but let loose a furious Big "NO!". Later, he was found frozen in ice by the Laughably Evil 1987 Shredder in Turtles Forever, which was proof that this was Ch'rell's fate, a fate eventually undone by the 1987 Shredder himself.
In the original cartoon, this was Baxter Stockman's ultimate fate- trapped in limob between dimensions.
The genie in Aladdin was stuck in his lamp for 10,000 years! But he doesn't seem too traumatized by the experience. Though he is a genie. For all we know, that's standard fare for them, if somewhat undesirable.
DVD commentary suggests that the genie keeps himself entertained by observing parallel realities and timelines, which is also why he's a walking popculture reference: he's actually seen our world and all the shout-outs he does are like an in-joke for him.
Upon losing a game, sprites and binomes alike can get "nullified" - in-universe, that means reduced to a deformed, slug-like creature that can't make any noise above a squeak.
Luckily, right at the end of the series, Phong almost perfected a cure. Until Megabyte takes over and the show is cancelled
The Medusa Bug episode, which proceeds to turn everything in Mainframe into stone.
In Mummies Alive!, Scarab murders the son of the Pharaoh in order to obtain immortality; since Pharaoh cannot execute Scarab, he has him entombed instead. The modern-day archaeologist who accidently frees Scarab from his imprisonment many centuries later notes that the walls have multiple tallies scratched into them, caused by Scarab counting out the days of his immortal existence.
The SpongeBob SquarePants episode "Perfect Chemistry" ends with Plankton being stuck in a corked bottle, in Mr. Krabs' safe, where no one can hear him.
The episode, "Home Sweet Pineapple" ends with Squidward trapped under Spongebob's house, unable to see anything or move.
Another episode features Squidward trapped in a cement cocoon for days.
This is the terrible fate Van Kleiss suffers in Generator Rex. His attempt to control time misfires when Breach interferes, knocking him through a vortex that sends him all the way back to Egyptian civilzation. In order to get back to the present, he constructs a "hibernation" chamber that uses his Nanites to halt the aging of his body while stayingfullyconscious for4,000 years. Worse, he's forced to recreate the chamber each time it cops out too soon all the way up to the present, painstakingly waiting through era after era for his exodus. If that wasn't bad enough, a spectral entity is chasing him though it's revealed to be a mutated Breach being dragged along each time he sits in dormancy. Eventually, it takes so much of a toll on Van Kleiss, nearly all of his Nanites have died and the isolation drives him to insanity, causing him to forget his own identity and purpose. When he finally makes it back to present day, he manages to recover his sanity little by little after Black Knight meets with him and tells him to get a hold of himself.
In the finale of Action Man, this fate befalls Dr. X, the Big Bad. He's gained superhuman abilities, doesn't need food or air any longer, and becomes Nigh Invulnerable... and then Action Man traps him on an empty rock floating in the immense vastness of space with no means of escape. He actually does scream Action Man's name one last time as the rock drifts away from earth.
In Ben 10: Ultimate Alien "Night of the Living Nightmare" Albedo gets a Cassiopean Dream-eater stuck on his head because he slipped on the spilled smoothie that Ben knocked over in the beginning of that episode. As if having a skull-faced alien jellyfish attached to his head wasn't bad enough, the Dream-eater traps him in a never-ending nightmare so it can feed on the chemicals his fear-addled brain produces. Said nightmare consists of an invincible Ben mercilessly beating him down.
The Penguinsof Madagascar has Skipper's previous teammates, Manfredi and Johnson, as exhibits at an Aquarium... and when he flies past them, he can't hear them.
One episode of The Secret Show ends with Doctor Doctor being tricked into sucking the entire universe into the Trousers of Doom! Because she happens to be wearing them, she is forced to float through the void all alone where no one can hear her.
In fact, one could argue that several things, such as the dinosaurs and the Atlanteans, that were sucked into the Trousers of Doom suffered this fate before the universe was added into the mix.
The fate of the Trix at the end of Seasons 1 and 3 of Winx Club. They are trapped in a virtual world full of positive atmosphere that they hate, which is shown to be driving them mad at the beginning of Season 2 before they are rescued by Darkar. Also of note, while the Trix return in Season 5 in most versions, the 4Kids dub ends with Season 3, so in its continuity the three witches presumably remain there for the rest of their lives.
Then there's Valtor/Baltor, who among many unnamed convicts is frozen in the Omega Dimension at the beginning of Season 3 before being released by the Trix. This was intended to last for eternity, and he was awake the entire time he was frozen.
Murderface's grandfather in Metalocalypse. Thunderbolt Murderface (that is his name) has had a massive stroke and was being pulled around in a wagon by his wife who rides a mobility scooter. After his grandmother guilt trips him into it, Murderface buys him his own blink operated wheelchair. Which he uses to say: "I've not had an erection in 30 years" and "I just used my underpants as a restroom" before just saying "Kill me." repeatedly.