The Big Bad Naraku had his body obliterated multiple times, but always regenerated before the end of the episode. Actually, for a big part of the series, killing him would have required killing his heart, stored in another being (He eventually just absorbs the other being because it tries to betray him). In the end, Naraku ended up Deader Than Dead when Kagome used the Shikon Jewel to wish Naraku's spirit out of existence along with the Shikon Jewel itself.
Kikyo was killed multiple times. The first she actually died but came back. The second time she fell off a cliff. Then she fell into a valley full of caustic poison. At a point in the story, she finally died forever when she dissolved in front of everyone.
Sticking with Rumiko Takahashi, in the world of the Mermaid series (Mermaid Forest, Mermaid's Scar, etc.). Anyone who survives eating a mermaid's flesh can basically only die if something happens to the head, a la Highlander. Decapitation is mentioned, while one immortal succumbs to total consumption in an intense fire.
The Ninja Scroll movie, features a Big Bad who can regenerate any part of his body — even decapitation won't stop him. Jubei therefore has to get creative when defeating him; He eventually does so by covering the villain's body in a thick layer of molten gold and letting the cooled statue sink — with his still-living body encased inside, presumably forever — to the bottom of the ocean.
Nasuverse is loaded with characters who cheat death in a variety of ways (being undead, reincarnating, etc...). The two Shikis, Shiki Ryougi and Shiki Tohno, can kill these things deader, because their eyes allow them to destroy their very concept of being. In fact, they can even kill things like ghosts, buildings, telekinesis, or appendicitis using a butter knife.
To be specific, they can kill anything they can comprehend the death of. Ryougi has Akasha helping her comprehend the death of some things, so she can kill anything that she can perceive as 'living'; Tohno, meanwhile, doesn't have this assistance (and thusis slowly being driven mad). In one of his endings, he kills Arcueid's connection with Gaia so that he stands a better chance of beating her while the moon is out. In another route, he is able to actually kill poison while it's still flowing through the bloodstream.
The series which cheapened death to the point where the main cast isn't all that concerned when the Big Bad starts killing off the majority of the planet's population, since they can just be wished back to life! It's implied that if one dies while already dead, they're really gone, but as this never happens to anyone we can't be sure.note In fact, in one arc, the Ginyu Force ended up impaled by the needle mountain that, by all rights, should have killed them again, but they didn't die. Cell did as well, although he had regeneration But there is one convention in the series, though: if the Big Bad gets killed by a Spirit Bomb (aka Genki Dama), you can even bet your TV Tropes admin rights that he's Deader Than Dead.
Actually, the idea that someone being died means they're gone forever is outright stated by King Kai, as Kid Buu was about to blow up the afterlife and everyone in it entirely, leaving absolutely nothing left to even be revived in the first place. And as for the Spirit Bomb, it has actually never killed a villain in series: it purified the only two that were thought to be destroyed, allowing them to reappear/reincarnate purified of their evil (Kid Buu into Uub, and Omega Shenron into Shenron respectively). Additionally, the sacrifice made to let the rest of the planet be killed was one of the few times Death stoped feeling so cheap, given that Majin Buu proved that he could kill the entire planet with all the effort of raising one arm. And with the person responsible for the cheapening of death being only a few feet away from him and all the main heroes pressumed already dead...
People who die of natural causes can't be wished back by Shenron, which is why Goku developing a heart condition during the beginning of the Android Saga was such a big deal. In addition, the original Dragon Balls had the rule that you could only have a given wish granted once, so anyone who died a second time would be dead for good. The Namekian Dragon Balls threw this limitation out the window, and had no such limitation on the number of times one could be brought back.
In Part 2, the villain Cars finally attains immortality near the end, and has to be "killed" by being knocked into space by a volcano, where he eventually stops thinking, effectively becoming Deader than Dead.
Hollows and shinigami are post-death beings. In short, ghosts. Although it's possible to kill them without actually cutting off their heads, they can potentially survive truly ridiculous injuries. As a result, the only way to be absolutely certain a hollow or shinigami is dead is to cut off the head. This can lead to extraordinary measures being taken to ensure the most powerful hollows or shinigami are definitely dead from their wounds and stay that way. Even then, being a Buddhism-influenced story, this will free the souls to continue along the wheel of transmigration, allown the soul to be reborn as a completely new being.
Quincies take this one step further than anyone. They don't simply kill hollows, they destroy the soul as well. They are the only beings that are capable of eradicating a soul from existence itself, meaning the soul cannot go on to be reborn into future lives.
The anime-only Bounts can eat both unsent and living souls. In fact, it has been noted that a Shinigami's zanpakuto is the ONLY thing that can help souls move on (not counting the natural transformation of unsent souls into Hollows).
In a rare case of this happening to one of the good guys, Shigekuni Yamamoto-Genryusai suffers this fate. After being sliced in half, and then getting his arm cut off as he clinged to life, his entire body is dissentigrated to make sure there's no come backs.
In the manga Fullmetal Alchemist, you must destroy the Philosopher's stone that contains the actual Homunculus instead of destroying its body (according to later chapters, the body can apparently survive on its own and absorb a new philosopher stone if it isn't killed afterwards. It seems to lose its homunculus powers, though). In the anime, a Homunculus must be killed once per incomplete philosopher's stone within them (or forced to expel them otherwise, and then die again), but are frozen in place (allowing all the time in the world to actually do this) when confronted with a piece of their original human body.
Then there's the Philosopher's Stones themselves, which still contain the souls of the people sacrificed to create them. Once their energy is used up, these people are gone for good.
Hotaru died five times during the series: One in her past incarnation (when she destroyed all Saturn's (or Titan's, in manga) life by the calling of the Outer Senshi's Talismans), one when she was a kid and one of the transdimensional experiments at her father's lab exploded, one when Mistress Nine took control of her body (but yet, Not Quite Dead), one when fighting against Pharaoh 90, and the last one when she had her Star Seed/Sailor Crystal taken. She ended it alive.
All of the evils and good guys of the series seem to be parts of some cosmic cycle and have died at least once, generally many more times. Further, all the normal inhabitants of Earth seem to be consciously absent by the time of the planar calamity and the Big Bad's attack, only to be very alive right at the moment of the Bad Guy's death. A few villains (Kaolinite, for example) and heroes are even revived mid-season and almost on screen. It seems like only the evils slain by Moon herself in this present incarnation are really dead. And not even all of them.
People die in Shakugan no Shana by having their "power of existence" consumed — i.e., removing them from having ever existed in the first place.
The Data Entities in Haruhi could delete certain events — and, to some extent, beings.
In Code Geass, Lelouch takes control of GOD and orders Him to wipe his parents from existence. More specifically, he begs "God" (the collective unconsciousness of mankind) to not take away mankind's future. "God" interpreted this to mean "Get rid of his parents"; since they were in a spiritual realm, this resulted in his parents dissolving from existence within the realm. It still qualified because it managed to remove Lelouch's father from existence: a man who possessed the "Code" and was essentially an immortal being.
In Naruto, several of the villains they face have some form of immortality or method of escaping death that requires extra effort. Sometimes on repeated occasions.
Orochimaru: The Naruto poster[[Was Once a Man...thing]] for defying death. He survived a close brush with the Shinigami, Tsunade's rock-shattering punches, and being sliced apart by an electric katana. He was believed dead after being struck with an attack which would trap him in an eternal genjutsu, but it turned out he imbedded fragments of his soul in the Curse Seals he applied to his minions. So long as one of those still exists, he can potentially gain a new host body.
Kakuzu: He has five hearts, all torn out of other shinobi. To kill him you have to destroy all of them before he tears yours out and adds it to the collection. It took a jutsu capable of destroying his body on a cellular level to put him down. That didn't kill him. He was still down on one (possibly faulty) heart. Kakashi eventually finished him off.
Hidan: Cut off his head and he complains about his hair getting pulled. He had to be dismembered, buried in an isolated forest, and left for a few years until his immortality jutsu ran out. And he still has time to roll his head back into action...
Word of God says that he is currently dying slowly of dehydration... and his head will rot before he eventually dies.
Hokages 1-4: All currently in the stomach of the God of Death, though it turns out the Uzumaki Clan had a counter for this as well.
Obito survived half of his body being crushed by a boulder as a child. As an adult he went on to survive a wide range of overkill attacks aimed at ending him and was even revived after being forced to use a jutsu that killed him. He finally died when Kaguya reduced his still-living body to ash, but that didn't keep him from giving Kakashi temporary use of the Sharingan from beyond the grave.
Digimon in general are fairly immortal, as most of them merely turn into Digi-Eggs after death. However, the Big Bad rarely ever return. The exception is Myotismon, whose soul persisted each time he died and regenerated into a more powerful form. The Digidestined finally manage to permanently kill him by vaporising his body and then combining the energy of every Digidestine on Earth to blow up his soul.
In Digimon Data Squad, Digimon turn into eggs as well, but Kurata is revealed to have created a weapon capable of corrupting a Digimon's data, so that the Digimon dies permanently.
Any Asura or Deva in Popcorn Avatar who goes against the rules of the avatar battles and decides to take matters into their own hands by manifesting in their true forms is forever barred from Samsara, the cycle of death and rebirth, and is literally erased from existence.
The backstory for the Marvel 1602 continuity is that, in a dystopian future where America is ruled by a despotical President-For-Life, Captain America joins an underground resistance-movement, fails, and is captured. The president then displays his Genre Savvy side - this being the Marvel Universe, killing an A-list Super Hero has a spectacularly low probability of sticking. So instead, he attempts to remove him from the timeline entirely. After shooting him in the head. Instead, Cap winds up being sent over 400 years back in time, thus altering the timeline and ushering in the 'Age of Marvels' during the reign of Queen Elizabeth the First.
This happens in the short story "Singularity Ablyss" in the Transformers Legends comic, ( which is set between-the-scenes of the Beast Wars episode "Spark of Darkness"). Megatron, after being defeated by Nightscream, has his spark approached by Rhinox's who attempt's to act as a spirit guide and redeem the tyrant, this failed however and Megatron charged his particles with "purity of purpose" and used the knowledge of his physical state to erase Rhinox's spark from existence.
Scud The Disposable Assassin featured a werewolf villain that seemed to regenerate from any kind of death, including having the main protagonist punch his way through the back of its head. The werewolf is finally defeated when it is jettisoned into orbit around the moon, where it explodes, reforms, and explodes again in an endless loop.
The casting of the Montesi Formula in the Marvel Universe not only destroys every vampire except Hannibal King in the dimension, it makes it impossible for vampires to even exist in the dimension — some brought in from another crumble to nothing as soon as they arrive. The Formula is uncast a few years later, since somebody always wants to write about Dracula.
In Those Annoying Post Bros by Matt Howarth, anything that dies in Bugtown regenerates, though sanity may be slightly reduced. (The crazier Post Brother says "Naw, I've died lots of times." Tactful silence.) In one case, a character is killed in the street and spends several months regenerating and getting run over before an opportunity to get out of traffic. To kill someone for real, you have to get him out of Bugtown somehow.
Don Hall (the first Dove of the Hawk and Dove duo) is so dead that the zombie-creating Black Lantern rings cannot so much as disturb the dirt around his grave. This is apparently because pacifist Don was "at peace" when he died, compared to most dead heroes who most assuredly weren't.
It's implied that this happens to the First of the Fallen from Hellblazer at the end of Garth Ennis' first run, after he's stabbed with a dagger composed of the energies of the now-killed Second of the Three and Third of the Three — he's the most ancient entity in the universe besides God himself, and predates any concept of mortality or an afterlife, so even he doesn't know what will happen to him when he's Killed Off for Real. This doesn't stop another writer from bringing him Back from the Dead — in one of the worst-received runs in the comic's history, and one that has never been released in Trade Paperback.
Chris Claremont has said this is the fate of anyone who gets killed in X-Men Forever— when Wolverine was killed off in Issue 2, his picture in the recap page was overlaid with a big red "DEAD" for at least 10 issues just to drive the point home. He did reappear, but only in flashbacks from his World War II service alongside Nick Fury.
And, he finally got to retcon the original ending for X-Men (vol.2) #3, in which instead of surviving, Magneto and any Acolyte who wasn't Fabian Cortez burn up and die in Earth's atmosphere as Asteroid M disintegrates.
In The Grievous Journey of Ichabod Azrael (and the Dead Left in His Wake), Ichabod is able to kill the grim reapers in Hell or limbo or wherever he is using a massive effort of will; they then get sucked down into what is believed to be a place even worse than Hell. It's implied that he can kill the already dead in a similar manner.
In the epilogue to Ultimatum, the writers go out of their way to assure everyone that not only is Wolverine really dead, extensive tests have been done to prove that he cannot be cloned, regenerated, or resurrected in any way. This after a Rasputinian Death.
The original Dr. Robotnik in Archie Comics' Sonic the Hedgehog wasn't just killed, he was vaporized by a weapon designed to lock onto and disintegrate the DNA of individual people. The only way he could return? Reality warping via nuclear echidna. No joke. The revival is only temporary, lasting a month before he dissipates again. Then came the Cosmic Retcon, in which Dr. Eggman altered Mobius' reality so much that Dr. Robotnik and Robo-Robotnik, Dr. Eggman's original form were disassembled through time/space and realtered so that Dr. Eggman always existed on Mobius.
In the finale of Marvel Comics' Universe X, the embodiment of Death itself was annihilated. While this, at first, seemed a victory, it quickly turned sour when many people who had suffered irrepairable injuries or incurable diseases found themselves trapped in endless suffering. This was especially to the chagrin of the already-impossible to kill Daredevil, who had made a living out of never dying, no matter what was done to him. Finally, a team of heroes and scientists manage to find Jude, the Entropic Man - and his touch, it is revealed, can end even Daredevil's life, turning him to inert atomic dust.
Happens to Phobos in W.I.T.C.H.: after he broke out of the unescapable prison he had been thrown into, did what he did in the Trials of the Oracle arc and subverted a Disney Villain Death in a way that nearly allowed him to steal their powers, the Guardians disintegrated his soul to make sure he didn't return.
The Punisher 2099 had a villain who claimed that upon his death he would absorb psychic energy he had accumulated in the population of the surrounding city and become a godlike entity. Punisher called up his tech guy, and after some research he came upon a hypothesis that a particle accelerator might actually be capable of destroying souls. So the Punisher threw the guy inside one and switched it on. Seems to have worked.
In Creature Tech, Dr. Jameson cheats death via a Deal with the Devil—he won't enter Hell as long as he has the claw of the demon Hellcat. He dies at the beginning of the comic but persists as a ghost, then finds a way to return as a revenant. At the end, the protagonists kill him off for good by cutting the claw off his dead body, at which point several demons arrive and drag Jameson down to Hell.
In Frau Trude, the little girl goes to a witch's house, where the witch turns her into a block of wood and burns her.
In The Three Citrons, a slave murders the heroine with a hairpin. When she returns as a dove, she has her killed and cooked. When she returns a third time, the king asks what sentence would be suitable for someone who harmed her, and the slave prescribes burning, and the ashes being thrown from the palace roof; so she is.
In The Death Of Koshchei The Deathless, the prince's horse cracks Koshchei's skull, and the prince finishes him off with a club; then he burns the body and scatters the ashes.
In "The Legend of Link: Lucky Number 13", gods are commonplace (including Link himself) and therefore so is resurrection. However, toward the end of the story, Ganondorf's soul is scattered across countless dimensions due to a Heroic Sacrifice. It would take a god millions of years to track down every last piece, and the one person who might want to try has already decided not to.
In Beetlejuice, ghosts who are exorcized go to the "Lost Souls Room", where they endure a disembodied existence described as "death for the dead".
The ghostly killer from The Frighteners not only kills humans, he can also kill other ghosts. As it turns out, they just go to whatever afterlife they had been avoiding by being ghosts in the first place.
In the original Highlander movie (1986) and the series, the immortals can regenerate from any mortal wound, and do not age. They can only be killed permanently by cutting off their heads (or presumably if their bodies are burned to ash too quickly for them to regenerate, although this is never explicitly stated in the movie). In fact, they have to die at least once to become aware of and "activate" their immortality, otherwise they'd spend their days as a mortal until they died from old age.
In The Mummy Trilogy the heroes spend a lot of time trying to find a way to kill off the undead High Priest Imhotep (played by Arnold Vosloo) for good. Not an easy task, since the mummy's body is virtually indestructible (when O'Connell cuts off Imhotep's arm, he merely puts it back on and it fuses instantly) and he can become invulnerable by transforming into a whirlwind of sand. In the end, the heroes perform an old Egyptian spell to split off the immortal part of the mummy's soul from the rest (in Egyptian belief, everyone had three souls) which is dragged into the Underworld. Afterwards, Imhotep, while still being undead, is now mortal and can be killed. Although Imhotep is resurrected and comes back from the dead again for The Mummy Returns and only finds permanent rest at the end of the second movie. (The third movie involves a different mummy.)
The Genre Savvy heroes of the Scream films always shoot the killer in the head, because in the movies, they always come back for one last scare.
The film The Neverending Story, the residents of Fantasia are worried about The Nothing. It's an absence... not just a hole. A Nothing. Those pulled into it aren't just dead, they are gone from existence. This made for a Ticking Clock and also Nightmare Fuel for a small child.
In Wreck-It Ralph, video game characters who die in their own games simply regenerate later. If they die outside their games, however, it's Game Over. For good.
The Last Apprentice series of novels has the creatures of the Dark be soulless and once destroyed, they can never return. One such creature is The Bane who was worshipped as a God, then trapped behind an iron gate, released from the iron gate, brought back to the iron gate (if he returns to the gate, he can never escape again, so already a Fate Worse than Death) and to top it all off, the main character impales the poor demon three times with his iron rod before causing the demon to explode and disappear from existence.
The Taltos novels of Dragaera see people die and come back all the time; "revivification" is a tricky spell but most nobles will be willing to have an emergency fund for just such an occasion. If you want someone to stay dead, cutting off their head or damaging their brain will make reviving them impossible, or you can always stab them with a Morganti weapon, which will eat their soul, not only preventing resurrection but also cutting the victim out of the cycle of afterlife and reincarnation that is the natural order of things in Dragaera. One of the few times where Deader Than Dead really means deader than dead.
In The Wheel of Time, the only way to be sure that the Dark One doesn't reincarnate the Forsaken, his lieutenants, is to kill them with Balefire, which retroactively erases them from the timeline a few minutes. This causes the Dark One to miss the window of opportunity to pull them back into the Pattern (time). In addition, killing a spirit residing in tel'aran'rhiod, the World of Dreams, causes that spirit to be removed from the Pattern altogether.
Deliberately subverted (somewhat) in the Young Wizards book series by Diane Duane, where the Big Bad is almost always just a particular avatar of the Lone Power, who is so ubiquitous as to be represented in practically every culture (including alien ones)'s mythology or folklore, usually as a Trickster God as its "gift" of death/entropy has to be accepted by each species as it gains sentience... though it is also rather blatantly a Lucifer figure too (Wizards greet him as "Fairest and Fallen", and his invention of entropy got him kicked out of the Powers That Be's godly clique). Then again, the same holds true of fellow Power "The One's Champion", who is intended to beat the everliving crap out of it in its own avatar in a number of key battles... over and over and over again.
Played straight in a slightly weird way in the third The Dresden Files book, in which an evil (and apparently quite dead) sorcerer's nasty leftover rage manifests as a ghost that wreaks havoc on the folks he blames for his defeat, and anyone close to them. This editor calls it a "slightly weird" way because Dresden Files ghosts apparently aren't actually leftover living beings' souls so much as they are single-minded metaphysical residue from the deceased's emotions and intent, as seen when the titular wizard deliberately creates one of himself to help get out of a nasty situation, yet manages to be side by side with it moments later after he's resuscitated.
This is further explored in Ghost Story. Ghosts are spiritual copies of the deceased, formed and powered by their memories. A sufficiently powerful ghost can use memories to augment their abilities or manifest into a physical form. This is essentially Cast from Hit Points, however, and a ghost who uses up too much of their memories can become a Wraith - a mindless being that feeds on other ghosts' memories- or cease to exist entirely.
They killed him good. A couple of times. He'd come back after they'd killed him early in the nineteenth century, so they were real careful this time.
Roger Zelazny's novel Lord of Light is set in a world where everyone, from self-styled gods to lowly peasants, can have their consciousness transferred into a new body for a price, in a technologically-assisted version of Hindu reincarnation; the now empty old body is cremated. To forgo reincarnation, or be denied it, is to "die the real death".
In Garth Nix's Old Kingdom trilogy, necromancers regularly bring back the dead, but dead generally lose all personality and sometimes their human appearance in the process. There are varying degrees of deadness, and once a person gets beyond a certain point, any resurrection of them will be a horrible monstrosity. The Abhorsen's job is to lay the walking dead to rest permanently by sending them beyond the Ninth Gate of Death, from which no one ever returns — even escorting them there personally, if necessary.
He was defeated in a way that's normally ignored: despite being the only vampire on-screen to survive being staked (twice), he was humiliated and left in disgrace.
In Terry Pratchett's Discworld book Witches Abroad, a village-raiding vampire is hit by a thrown garlic sausage while in bat form and, while stunned, eaten by Nanny Ogg's cat Greebo. The narration later mentions that while vampires have risen from the grave before, none have ever risen from the cat.
One of the mushrooms described in The Discworld Almanac falls just short of this trope: it's said to be toxic enough that someone who dies eating it may still arise as a zombie, but a zombie that will still feel very sick.
The traditional method of execution for the Witted in the Farseer trilogy consists of hanging the victim over running water, chopping them up, and burning the pieces to make sure they're dead. It's also not really needed, Fitz's return from the dead notwithstanding.
Mostly Harmless was written on the condition that Douglas Adams be allowed to destroy everything so utterly and completely that it would never ever ever come back and he would never ever ever have to write in that world again, making the entire earth Deader than Dead.
Daemons and daemonhosts from the Warhammer 40,000 universe are generally just banished back to the Warp when their physical bodies are killed. So it's especially notable that Eisenhorn managed to kill one (Prophaniti) so thoroughly that it was erased from existence, Warp presence and all, at the end of Malleus.
The Emperor killed Horus by obliterating his soul so he can't even reincarnate by the will of the Chaos Gods.
Abaddon managed to get a piece of the action too, by destroying the body of Horus and the cloning facility designed to revive him so thoroughly that no one dared to even mention Horus's name in his presence ever again.
In the Black Jewels world, if one of the Blood is powerful enough, they can continue to inhabit their body after death, and are called demon-dead. This is why it's important to "finish the kill," or burn out the person's Jewels (source of power) and brain, so that someone you killed last Tuesday doesn't track you down later to return the favor.
Septimus Heap, nearly every dead person in the Septimus-verse comes back as a ghost; it's just how things work there. Exceptions include:
Series Big Bad DomDaniel has died and been brought back a couple times, including in a couple ways that are freakishly gruesome for a kid's series. However, in Queste, he is eaten by Spyt Fyre the dragon and obliterated so thoroughly he doesn't even leave a ghost.
In Physic the same thing happens to Etheldredda, who is killed with a dragon fire-based spell.
In the Dream Park novels, participants in high-tech adventure LARPs who get "killed" are designated as slain by a black holographic aura. In The California Voodoo Game, a zombie struck down by the Gamers is immediately cloaked by two overlapping black auras, indicating it's this trope.
Also from California Voodoo: areas of MIMIC that are off-limits for players are marked out with "radiation" symbols. Any character who violates a "radiation area" is not only killed without a saving throw, but their character is permanently declared dead by the International Fantasy Gaming Society, never to be played again.
In the Takeshi Kovacs series people have cortical stack implants that act as hard drives for their brains so that when they die they can be resleeved. Even then many characters are subjected to "true death" by having their stacks destroyed or wiped. The wealthy often have off-site backups, but even those can be taken out.
Trapped on Draconica: Dronor can invoke this: his fire can erase someone from existence. It is the highest punishment he is capable of administering.
The protagonist of the classic horror novel The Night Land seems more concerned about being "destroyed" than killed. The implication is that being killed allows one to go on to the afterlife, while nothing follows being "destroyed".
In A Song of Ice and Fire, resurrection is possible (though rare enough that most people assume it to be legend, and are astonished when it happens), but only if the body is in good enough condition. In particular, decapitations are mentioned to be permanent deaths.
In the book, the Sword of Shannara, the Warlock Lord died, and has been driven back multiple times. However, the Sword of Shannara, with the power of the Awful Truth finally forces him to acknowledge that he was dead, animated only by his own willpower.
Live Action TV
Buffy the Vampire Slayer: The Master. When he was staked, his bones were left behind. To make absolutely sure he's gone, Buffy smashes them to dust with a sledgehammer (but it didn't work). Counting Expanded Universe, he's had his soul destroyed twice.
Claire Bennet of Heroes can regenerate even from apparent death, but she can be put into a state of death indefinitely by sticking a foreign object in the base of her brain and keeping it there. The "save the cheerleader" subplot also implies she could be permanently killed by having her brain removed, and Peter's encouraging her to shoot him if he goes nuclear (after he absorbs her healing power) suggests that either of them would also be killed by having a certain part of their brains obliterated. Fans have jokingly suggested that the base of the brain is where the "regeneration gland" is located.
Later Sylar even moves his "regeneration point" using Shapeshifting, making him virtually immortal.
Stargate SG-1 employs this concept several time. First, with the villain Apophis, who continually escapes death, even going as far as being raised from the dead by a rival, assassinating said rival, and taking control of the dead rival's army. He is finally killed permanently when his spaceship crashes on a planet while he is trapped on board. The villain Anubis is immune to death because of his former status as an ascended energy being, effectively rendering him "Touched by Vorlons", before finally being taken out of the picture by his "Vorlon" sacrificing herself to restrain him). On the non-villainous side, Daniel Jackson dies repeatedly throughout the series. He is brought back several times via the Goa'uld "Sarcophagus" device and then later by ascending to a higher plane and then descending back to human form again. Several other major protagonists suffer non-permanent deaths as well, including one incident where O'Neil is tortured by Ba'al by being killed and resurrected over and over again.
In Doctor Who, the Master is killed deader than dead repeatedly, and quickly gained Joker Immunity. After a while, they stopped even trying to make excuses. On one of his later reappearances in the original show, he has the immortal line "I'm indestructible, the whole universe knows that!" and that's all we get for an explanation.
There is a Time Lord weapon, the De Mat Gun, which can accomplish this. It effectively erases the target from history, so that it never existed in the first the place.
Subverted in Doctor Who: The Curse of Fatal Death (which was both a comedy and a tribute); both the Doctor and the Master clarify that no one can regenerate after being slain by "Zektronic Energy", but of course, the Doctor "gets better" anyway. (The Master is shocked: "It's against all the laws of the Universe!", to which the Doctor's companion replies, "Perhaps even the Universe can't stand to live without the Doctor".)
Most enemies in Doctor Who are like this, but not on the individual level. The fan favorites always return. Try counting how many times the Doctor says "You're the last of your kind" to the Daleks in the new series. And then watch as 2 episodes later the last of the Daleks make a return... only to be killed and for another group to take their place. It's well into season 3 before they establish a proper storyline that sets up the next Dalek plot.
Season 5 has Rory, who dies and gets erased from existence. He still manages to come Back from the Dead.
Amy: You think you'll just come back to life? Rory: When don't I?
In True Blood the vampire leaders sometimes give other vampires what they call the True Death by beheading and staking the vampire to be executed. (Sunlight also works).
The Cylons in the new Battlestar Galactica series download their consciousness into a new identical body when they die. How exactly this works is never fully explained. It is hinted at that all Cylons get resurrected, including the semi-biological self-piloting Raiders, not merely the twelve fully biological human models. (Although it is unclear if this is also the case for the completely robotic Centurions). For the process to work, a resurrection ship or resurrection facility has to be in range, so if a Cylon dies in space beyond range, he or she is permanently dead, their individual memories and consciousness lost to the collective. In addition, the Cylons deal with rebellious members by "boxing" them, where they download their consciousness into a small metal box and then put the box in storage. Also, season 4 sees the beginning of a Cylon civil war, one of the first acts of which is the luring of several ships into an ambush and destroying them while out of range of the Resurrection Ship. This is presented as a particularly heinous crime to the Cylons, who understandably have something of a blasť attitude toward death.
In Blake's 7, actor Gareth Thomas (Roj Blake) appeared in the final episode of season four, "Blake", on the condition that his death was sufficiently graphic to rule out a return Back from the Dead. Ironically, this proved unnecessary as there was no season five.
To make sure Gareth kept asking the pyrotechnic crew to add more bullet squibs to his chest plate, leading to a quite painful result when they went off.
In Supernatural there are a few ways to bring someone back from the dead (none of them much fun) but it looks like anything shot with the Colt is staying down. Except for Lucifer. And although the Colt isn't used on them, the Horsemen of the Apocalypse are apparently immortal - Death in particular is incapable of being killed or incapacitated by absolutely anything under the sun.
Killing a ghost is basically killing an already-dead person. As is killing a monster in Purgatory, the monster afterlife realm.
In the Angel TV series, Fred is infected by an elder demon and consumed from the inside out, everything aside from her skin and hair replaced with something else and changed in color. Oh, and her soul is destroyed in the process, though it seems as if some part of her has imprinted on the demon, giving it at least one of her personality quirks in that she is fond of Wesley.
The demon had appropriated her body, and the subject of mind/body dualism is beyond the scope of this entry, but memories and emotions are all stored in the brain, which is part of the body. Sometimes Illyria deliberately accessed Fred's memories.
The episode following Fred's death beats the viewer over the head repeatedly about exactly how dead Fred is. It seems every other minute, the viewer had to be reminded that Fred was very incredibly dead: Her organs were boiled and burned up inside her body to feed Illyria, making it inhospitable for a human soul to reside in, and Fred's soul itself was devoured by Illyria as well.
The original plan, had the show gotten a new season, was to split up Fred and Illyria. In other words, it would turn out that Fred's soul was NOT destroyed after all. The comic books feature Illyria but not Fred.
Pushing Daisies: Ned can bring the dead to life with a touch, but if he touches them again after that, they die again and nothing can revive them. Also, one episode implied that if a body is in a particularly severe state of dismemberment, his touch won't work. Or possibly he just didn't want to bring back someone in that many pieces.
Torchwood in series 2 has just a bit too much fun with this one. First Owen is killed via gunshot wound then he's brought back to life. And if that's not bad enough he fights with Death itself, proving that he really is undead only to be vaporized in the season finale.
Then there's Captain Jack, who twice appears to have permanently killed before resurrecting: once at the end of the first series (he stays dead for a couple of days that time), and again in "Children of Earth", when he's blown to smithereens and his body still reforms in a truly gruesome fashion. It's eventually established that nothing will make Jack Deader Than Dead unless he is in fact the Face of Boe, in which case he'll finally die for good in a few billion years. Maybe.
Only one character from Charmed managed to have greater Joker Immunity than Barbas the Fear Demon, and that was Cole. Cole survived many apparent deaths that would have killed off any other demon for real, and this tendency to survive was Lampshaded on many occasions. He did finally die, however, from an incident in which he created an Alternate Reality where he was not quite so indestructible as he is in the normal reality. History changed in such a way as to keep him from being indestructible, and only then was it possible to vanquish him for real. Cole's only subsequent appearance was when he took on the form of a spiritual ghost who was dead rather than Back from the Dead as with his previous returns.
He still managed to be quite solid near the end. Fixing history should make him indestructible again, but he's learned that chasing Phoebe will get him nowhere by now, and gets to walk away on a good note.
Religion and Myth
In the book of Revelation, in The Bible, everyone will be resurrected at the end of the Millenium, to stand judgment. The damned, though, will then be thrown into the Lake of Fire, of which an angel has already told the visionary, "This means destruction." No more resurrections.
More specifically, it is called the 'second death', a phrase that, by that time, had been used in Jewish culture to describe an utterly irrevocable death.
A very common interpretation is that the damned will be restored to their bodies, but they will still be corpse-like, and it is only for them to now suffer physically and spiritually in hell.
In Norse Mythology, slain warriors may go to Valhalla, there to enjoy themselves feasting and fighting, rising again even if slain. But all that is just while waiting for Ragnarok, the final battle in which they will fight beside the gods and die with them.
In the Yu-Gi-Oh! TCG, "Eternal Rest" is a Spell/Magic card that destroys all Monsters holding Equipped-Spell Cards. Really Eternal Rest is a Trap Card that has the exact same effect, ostensibly to dissuade an opponent from just Equipping more of his Monsters, because there's No Kill Like Overkill.
In the earlier days of the game, removing monsters from play had this effect. Nowadays, the game has some cards which can even return removed monsters, and there is even a deck theme (Different Dimension) that thrives on doing so. For the most part, though, removing from play still counts.
This is also a gameplay mechanic. Here, killing something deader than dead is called being removed from play (banished as of recently). It's frequently used to pay costs for cards like Dark Armed Dragon, but it's just as often weaponized with cards such as Dimensional Prison.
Also common in Dungeons & Dragons, where resurrection is pricey but doable. There are several ways to make it impossible, though.
Spells which destroy the body completely, ie. Disintegrate, remove the chance for a simple Resurrection spell.
Liches should be mentioned specifically. Not destroying their phylactery just causes their body to reform.
A lich can also become a demilich, which can rip out people's souls at will. And digest them. After 24 hours, they're gone for good.
At least in 2nd and 3rd edition, it was frequently mentioned that one of the components for the ritual of lichdom a wizard had to make was a potion of extreme deadliness. So deadly that, if the wizard fails in his bid for lichdom, he would die, and the gods would not be able to resurrect the fool if they wanted to.
There is also a one-of-a-kind monster known as the Tarrasque. The writers probably put it in there to serve as walking Armageddon. It regenerates with lightning speed, most spells simply bounce off its hide, death effects won't work on it, and if you batter it to death, it'll come back in a few days unless you also used a wish/miracle (level 9, most powerful non-epic spells in the game) to make it stay dead. The books further note that even this doesn't finally kill the Tarrasque, but pushes the Reset Button on its cycle of sleep-wake-rampage-sleep. This being D&D, however, enterprising players can turn it permanently into something small, then put it in a secret chest spell for long enough so that it is erased from existence, etc. etc.
Unname, a spell which destroys the target's true name, altering reality so that the creature cannot exist.
There is another version of that spell that requires you a feat to take "Mother cyst". It kills the person and then destroys their soul, removing them from existence forever. Although it seems less useful at first glance than Unname since you have to hit the person with a level 2 spell first. It can be used in campaigns that are not using the 'True Name' system. Meaning it's just as legit in Eberron as it is the Forgotten Realms.
4th Edition's Tarrasque cannot be killed. It's so powerfully linked to the world that if you actually manage to bring him down to 0 HP, then he simply sinks back into the planet's core and sleeps again. The only way to really kill it is to somehow lure it into another plane or otherwise away from the world before killing it, and that's just a theory.
In the Epic Level Handbook, there is a special assassin guild called the Garrote. You contact assassins if you want a person to die, you hire the Garrote if you want a person to stay dead. (Specifically, they destroy their victims' bodies beyond resurrection, and in cases that require a 100% certainty, they bring the bodies to the head of the organization so that she can remove them from the multiverse altogether.)
Starting in First Edition AD&D, the Sphere of Annihilation will utterly destroy any being it comes in contact with, and presumably that being's soul. ("No spell can bring the dead character back to life, not even a wish!")
The chapters of the D&D rulebook Manual Of The Planes that are about the afterlife describe what immunities the souls of the dead have, implying that they can be slain in combat by those who visit the afterlife.
In the 2nd Ed. Planescape (set partially in the afterlife after all) rules the souls of the dead could be encountered, and killed. In many cases these souls were permanently dead. Natives of the afterlife killed outside of their native plane would reform on their plane, but if killed on their native plane were permanently dead.
The Leviathan, an Eldritch Abomination mentioned in the Elder Evils suppliment, has an ability called True Death which destroys the soul of anyone who dies within a hundred miles of one of its aspects. Fortunately, it only has this ability if its Sign is at Overwhelming intensity. (Which as far as Elder Evils go in a campaign using one, the Final Battle against it is about to begin.) The True Death ability is available for D Ms who want to create their own Elder Evils, but Leviathan is the only example presented in the book who has it.
Promotional material for Expedition to Castle Ravenloft, a 3E updating of D&D's most infamous and hard-to-eliminate vampire, urged players who dared to tackle Strahd von Zarovich: "This time, make sure he's dead dead!"
When you are doing favors for gods, especially evil ones, often if a character dies, his or her soul will belong to said god. Resurrection would be impossible. Unless you killed the god.
Which requires you to go to their plane and kill them. Without critical hits. Or ongoing damage. Or instant death attacks. Must I go on?
A natural death by old age cannot be undone by any means.
In the 4th ed. "Demonicon," it's said that, when a demon lord dies in the Abyss, and the Abyss is tired of playing with said ex-demon lord, a tomb materializes in the layer known as the "Blood Rift." The tomb is inevitably filled with the deceased's favorite possessions, both treasure and servants.
The Old World of Darkness game Mummy The Resurrection had the character playing (oddly enough) mummies, immortals who could die any number of times and come back to life, even if their bodies have been burnt to ash or pounded to dust (though it's really hard to do, then). Even their souls were similarly tough, being able to survive Oblivion. As such, the game lists (it's a short list) ways you can really get killed: suicide (not Heroic Sacrifice, actual "I don't wanna live" suicide), losing all permanent Willpower (see suicide), or extremely powerful magic separating the body and soul (like being eaten by Ammit). The only non-magical means of killing a mummy permanently is a point-blank atomic explosion (mummies can come back from dust or ash, but not subatomic particles), and that just traps them in the underworld.
In Demon The Fallen, killing a demon's body won't kill the demon itself. It will carve out a significant chunk of the demon's power and lash it with Torment, but the demon itself survives - though they go back to Hell if they can't find a new body or host quickly. However, if they die too often, they dissipate into nothingness... and while they're out of their host, any other demon can devour them, destroying them for good and taking a portion of the devoured demon's power.
Two special cases in the New World of Darkness are vampires and Prometheans. Inflicting what would be mortal damage to a vampire merely sends it into a deathlike sleep called torpor, from which they eventually awaken... unless fire, sunlight, or extreme mutilation (think decapitation or woodchipper) is used to finish the job, in which case they're the Trope Namer for Final Death. Prometheans, meanwhile, all come with one built-in resurrection (which burns all but one dot of Azoth), and can learn a power called Revivification (Osirans innately start with it) that sacrifices itself to bring them back; while they have it, they may give up dots of Azoth to pull slain Prometheans back as well. Even these aren't foolproof, though - fire does to them as it does to vampires (those powers need corpses to work on), they don't get the one-shot resurrection if they only have one dot of Azoth, and certain Pandoran abilities (including one that involves eating them alive) will do the trick permanently. Furthermore, Prometheans don't have souls (most of them spend their existences trying to earn one), so if they die permanently, it's lights out.
Amongst mages, on the very rare occasions it's deemed necessary to render someone Deader than Dead, they do so by removing that person's soul, traveling to the end of the Dreamtime, and throwing it away in the primordial ocean at the end of reality. This is considered the most abhorrent thing possible for a mage to do (for obvious reasons), and if it is ever invoked, the local ruling council will always voluntarily resign as an indication of their ultimate failure.
Book of the Dead, being the NWOD sourcebook for the Underworld, introduces two ways to render something Deader than Dead. On the one hand, there's the Crushers in The Junkyard, which are explicitly capable of killing anything. On the other hand, there's the Grave Dream, a repository of dead dreams which can be dreamed into in addition to the usual route of navigating the Underworld, where the very first Old Law listed is "Dead In, Dead Out."
In Warhammer, when the Great Necromancer Nagash was killed (chopped up with a magic sword so lethal it killed its user) the skaven dismembered his body, burned it with Hellfire and sent the ashes to their agents in various places around the world to scatter on the wind. And after over a thousand years, he still manages to return.
And then he gets killed again by the living god Sigmar, only to return after another thousand years. Nagash has at least three soul jars that keep him bound to the Warhammer world. On the bright side, he always comes back weaker than he was before (though he's still one of the deadliest things in existence), and he spends those thousand year vacations trapped on a spirit plane where the ghosts of everyone he's ever killed torment him constantly.
Unhinged, a very definitely not tournament-legal expansion of Magic: The Gathering, addressed the inflation of such things:
AWOL: Remove target attacking creature from the game. Then remove it from the removed-from-game zone and put it into the absolutely-removed-from-the-freaking-game-forever zone.
Which lampshades the fact that it's not at all hard to 'recycle' cards in the graveyard in this game and that even the generally accepted method of rendering something Deader than Dead by removing it from the game isn't 100% foolproof.
A recent rules change finally addressed this, and created the "Exile" zone to replace the "removed from the game" zone. Cards that allow the player to bring in a card from "outside the game" cannot affect the Exile zone, like they could with the "removed from the game" zone. This has had the effect of making the Exile zone more deader than dead than actually not being in the game at all. Some exiling cards, such as Necropotence, return the card to play later; Flicker does so immediately. (It's still useful; it stops stealing, gets rid of auras and counters, and all sorts of other fun.)
It doesn't stop there: some spells can make something deader than Deader Than Dead. Those spells exile a card and all cards with the same name from all zones of the game, including library and graveyard. It's less about being dead and more about having its very concept deleted from existence.
Inconsistent plotting in the books made Word of God have to emphasize that Yawgmoth, the Big Bad for most of the game's run, is indeed deader than dead. As he'd become a god and lived for thousands of years, only to be barely defeated during the Apocalypse storyline, and show up later to Karona (retconned so that it was All Just a Dream), many players to this day assume Yawgmoth will come back.
The Final Rest spell from GURPS: Magic is a positive take on this. When cast on the deceased it prevents resurrection but more importantly stops necromancers from abusing it for their purposes.
In Deadlands, anyone/anything that dies moves to the Hunting Grounds - essentially a spirit counterpart of the material world. From there, it is possible to eventually reach Heaven or Hell, but even that does not have to be permanent. However, upon "killing" someone in the Hunting Grounds you have two options. They can serve you for seven years (absolute-obedience-no-questions-asked style), or you can devour them. At which point you absorb their essence and they utterly cease to exist.
If Ming I, the Queen of the Darkness Pagoda from Feng Shui, hits you with her dreaded Arm of Darkness and you fail the Death Check that getting hit forces you to make, you are instantly and permanently destroyed — you don't come back as a ghost, no schtick can save you or bring you back, and your spirit can't be contacted from beyond the veil. You are, for all intents and purposes, gone.
Also, the Special Ability of Shiki Tohno (yes, that Shiki) kills something Deader Than Dead and makes it impossible for opponent to call the character he killed this way.
Eclipse Phase is a similar situation to Takeshi Kovacs (see literature), except that backups are more common making it even more difficult to kill someone permanently.
Exalted: while death is permanent (you might be able to become a Deathlord, but you can never be truly alive ever again), virtually anything that goes down the mouth of Oblivion is not coming back out. Characters can survive with perfect defences, but as soon as the motes run out, there's nothing left but memories.
'In Paranoia, each character has a genetic template. Every time someone dies, a new body is grown in a lab and implanted with the memories of all their predecessors. One becomes Deader Than Dead if one's genetic template is erased from the system, which may occur if one commits sufficiently egregious treason or by accident or sabotage.
And if the Computer discovers you have Machine Empathy, erasure of your genetic template is only the last thing it will do to you.
In Might and Magic, your party members can die. But that's not enough for some enemies, which can leave your party members ERADICATED, as in their bodies completely disintegrated. Resurrecting party members in that state is much more difficult.
Albert Wesker takes two RPG-7 rounds to the face while hip-deep in magma at the end of Resident Evil 5. It took Word of God to convince fans that he was REALLY dead this time.
The main character of Planescape: Torment regularly dies and revives just as easily. Much of the game is spent figuring out how this is possible... and under what circumstances the reviving might stop.
In one of the endings, you do this by willing yourself out of existence. That's one of the good endings, even.
If the Nameless One (which means you) tries to test the boundaries of his immortality on... let's say, Lothar or the Lady of Pain, s/he will promptly erase the Nameless One (I mean, you) from existence and you get a game over. The former is an immortal similar to the Nameless One but without any of the irritating side effects. The latter is the caretaker of Sigil who happens to be more powerful than almost any deity within the confines of the city, and will perceive the Nameless One a rash that has to be removed should the Nameless One overstep his place.
Several of the characters in Final Fantasy X, most notably Seymour (after the party kills him) and party member Auron (from the beginning), are actually "unsent" — souls that have not passed to the the local afterlife, the Farplane. As such, the only way to dispatch them permanently is to have Yuna "send" them; this isn't a harmful or painful process, but a soul generally can't come back from the Farplane afterward, and the targets in question are usually rather hostile about the prospect.
In Final Fantasy VII, Sephiroth's human body died five years before the events of the game and his body was dissolved in the lifestream, but his soul fuses with Jenova and is reborn. You then end up killing his reborn body at the planet's core. Then you kill his soul in form of a grotesque mutated angel. THEN Cloud kills Sephiroth's astral form in a one-on-one duel in the Lifestream. No other villain in the series has the honor of being this dead.
In Suikoden II, a vampire called the Neclord comes Back from the Dead. In response, about five different powerful beings map out every single contingency and possibility of escape so that this time, when they kill him, it doesn't happen again.
In the Roguelike game TOME: Tales of Middle-Earth, after you kill Tolkien's Satan Morgoth, you have the option of entering the Void and killing his soul to prevent a Ragnarok-style war in the future. While traversing the Void, you might have to randomly fight any boss character that you've killed before.
In the Mega Man X series, after being killed and resurrected as many times as Zero, Sigma is considered gone for good in the final game X8. Because his decimation took place on the Moon's surface, where the Maverick virus isn't as potent, Sigma is denied his ability to regenerate again.
All the characters in Grim Fandango are Dead to Begin With, but there are apparently several ways to suffer "death within death", like being crushed, or shot with a sproutella gun (which causes the body to be replaced by a forest of quickly-growing flowers - marigolds, to be specific, as a reference to the Day of the Dead).
Kingdom of Loathing spoofs this kind of public domain death with the boss monster Ed the Undying. Killing him for the seventh and final time merely results in his crumpled form growling angrily at you while you nonchalantly sweep him up in a dust-pan and leave him leaning on the side of the tomb, too exhausted to try and figure out a way to permanently do away with him.
In Phantom Brave, Marona can kill the souls of her Phantoms if they "die" and she herself attacks their... um... phantom corpse. She can still put the pieces back together though, and transmigrate them into a stronger form. She can also do this after the Bonus Boss Baal, after he attempts to possess the Possessed One, and discovers that this just puts him completely under her power. If Marona Soul-Kills him and then examines his "remains" the game states that the area is finally peaceful and calm. Given that in other Nippon Ichi games, Baal is a Physical God capable of coming Back from the Dead instantly, Marona really accomplishes something by permanently destroying one part. Although Baal does have more than one body.
In the computer RPG series Ultima, the protagonist (and party members) can easily and frequently be resurrected as necessary. There are a few points in the plot where it is possible for a character to be permanently slain - if taken prisoner by Blackthorne in Ultima V, and Dupre during the plot of Ultima VII Part II. The much maligned Ultima IX undoes the latter.
Dupre's death in Ultima VII Part II should be clarified, his death involved being turned to ash in a crematorium, and then his soul was used as a bonding agent to reform the chaos serpent in order to bring balance to the cosmos. Deader than dead because his soul was turned into cosmic superglue. (His subsequent existence as a ghost and resurrection in Ultima IX left planet-sized plot holes, and many of them, which caused some people to be... a little upset.)
While resurrection is by no means impossible, it's not as easy as in certain other settings. It's either extremely expensive in a very stingy setting or very costly in terms of power and resources - and it always leaves the newly-raised character near death, at 0 or 1 hitpoints. In Ultima III, resurrection can fail and leave you with a pile of ashes, playing this trope straight; the ashes can be Recalled, which is even costlier and permanently drops the caster's stats if you do it yourself. Ultimas V'' and VI follow every death with a loss of experience.
Classic text adventure game Adventure Land sends the protagonist to a place called "Limbo" when killed, from which egress is quite easy once you figure out how. There are only a handful methods of dying that really don't allow this.
Likewise, the Enchanter Trilogy provides you with spells (or allies) that automatically resurrect you upon death, but there are a few ways around this if you really screw up. Examples include erasing yourself from existence with a Time Paradox, having your soul eaten by a demon, and getting stuck in a permanent nightmare so that you aren't technically dead, but you might as well be.
The Elder Scrolls IV: Oblivion: Umaril the Unfeathered, main baddie of the Knights of the Nine add-on, is allied with the Daedric Lord Meridia and can eventually return to the physical world if defeated; it takes the Champion of Cyrodiil, eight holy relics, the blessing of a ninth and defeat in both the physical and spiritual planes to kill Umaril for good.
In the Kingdom Hearts series, when a Nobody is killed, they utterly cease to exist, not even leaving a body behind, in a surprisingly gruesome disintegration, usually accompanied by an elemental explosion and screaming.
Lampshaded in a dramatic way when a very young (a few dozen days old) Roxas ask Xibar the classical infant-question, where the hearts belonging to the deceased of the slain Heartless go. Kingdom Hearts. He then proceeds to ask, where deceased Nobodies go... And is "shocked" (as far as this is possible) to hear that deceased Nobodies go nowhere, won't return, and can't be met again. This severely depresses Roxas, as he's thinking that one of his only two friends, Axel, was recently killed.
According to Word of God, Nobodies that are killed after their Heartless will reunite with their heart and be reborn as a complete person; oblivion only comes to Nobodies who are killed with their Heartless still running around.
And as of Kingdom Hearts 3D, it's been revealed that Nobodies will literally grow a new heart after a while. Xemnas was aware of this and lied to the rest of Organisation XIII in order to stop them doing exactly that.
It's also what happened to Vanitas, sort of. He was actually the dark half of Ven personified by Master Xehanort. At the end, he attacks Ven to forge the X-Blade (you need two hearts of pure light and pure darkness, respectively, to do that). Ven defeats him in the preliminary battle, but Vanitas overpowers him with the Unversed and starts a conflict in the former's heart. Ven overpowers Vanitas and destroys him, destroying his own heart in the process.
In Baldur's Gate 2 when confronting Irenicus in Hell, he claims that to die there is to cease to exist. As it turns out he's wrong, and he ends up in another Hellish dimension, where he is attacked and possibly killed by demons. Whether he's really gone then isn't clear, though he never appears again to you.
The series generally inverts with the Bhaalspawn, who can be killed permanently in the normal fashion, whereas everyone else can be raised under the AD&D rules... except that Imoen ignores this rule and both Sarevok and the player character manage to claw their way back from Hell, although the latter wasn't properly dead.
In the .hack game series, one recurring boss, Cubia, is fought and defeated a significantly annoying number of times, only to suddenly get up after being killed and escape.
Zouken Matou escaped death in Fate/stay night despite having his body destroyed over and over so many times that its doubtful anyone believed he was really dead when Sakura pulled him out of her heart and smashed him. Therefore, they had Ilya/Justizia show up and tell him to hurry up and die already. Finally, he complied and just to make damn sure we know he's gone, they dropped a pile of rocks on him.
Another example could possibly be Gilgamesh's Ea. Ea's description indicates that it works by spinning so fast that it draws in air and compressing air so hard that it creates a time and space rift.◊
"The rift created by Enuma Elish is said to be a look at the "truth" of what existed before the world. Referring to it as hell, the primordial form of the planet before heaven and earth were split, a land filled with lava, gas, scorching heat, and intense cold, Gligamesh states that it is beginning of all legends of lands of the dead. It is the origin of the memory of all organisms before the existence of the planet that is no longer found in the imaginations or spoken memories of people, but rather a genetically inherent and repressed knowledge of a place and time when organic existence had been impossible."
It is said to have split heaven from earth, and is the only weapon to be designated a anti-world weapon. One presumes that if Ea was ever used at full power then the whole world would be Deader than Dead.
The Pile Driver in Boktai is an enormous Wave Motion Gun that channels solar energy created to kill the absurdly tough vampires that plague the world in a way that prevents them from reviving.
Except, of course, for The Count. Django had to become a Physical God to completely annihilate the guy, and even then he implies he'll be back before he dies.
In Diablo II, the player has to kill the Prime Evils, three demonic rulers of Hell, and destroy their Soul Stones to keep them dead. However, with the third installment of the series forthcoming, it remains to be seen whether it worked.
The soulstones were primarily prisons for the souls of the Prime Evils, because usually, all killing them does is send them back to the Burning Hells. They were corrupted, however, thanks to Izual the Betrayer, who filled them in on the soulstones and how to corrupt them, and helped the Prime Evils mastermind their own exile into Sanctuary.
And for the record, destroying the soulstones didn't take. You can thank Adria for that, marking each of the souls of each of the defeated so they would be drawn into the Black Soulstone of the third game.
In Diablo III Diablo himself, along with the other Prime Evils that were reincarnated into the reborn God of Evil Tathamet are slain for good by the heroes who wield power surpassing that of angels and demons. The ending depicts the monster disintegrating into nothingness as it falls.
Even that didn't take. Tyrael says at the end of Reaper of Souls, after the Black Soulstone is used up, that Diablo will reincarnate eventually.
At the climax of Mass Effect 1, Shepard must defeat Saren either in combat or by convincing him that Sovereign has been using him. Either way ends with a bullet in Saren's head. Shepard then sends a party member to shoot him in the head again "to make sure." Sovereign then assumes direct control of Saren's bionics for the Final Boss battle. Only after that is Saren well and truly dead.
In The Dig, a game whose premise involves an alien technology that will bring people back from the dead, it is stated that after several resurrections you aren't able to be brought back anymore, effectively making you deader than dead.
In Dragon Age: Origins this trope is the entire purpose of the Grey Warden order. Archdemons (corrupted gods who unite the darkspawnhorde) body jack the nearest darkspawn upon death, reviving almost instantly. Grey Wardens intentionally introduce a modified version of the darkspawn taint into themselves so that when one of them takes the final blow, the Archdemon will attempt to possess its killer rather than a real darkspawn, an act that annihilates both the dragon and the Warden's souls. Without this, the only way to end a Blight would be to kill every darkspawn in existence.
In the Sorrow duology of the Castlevania franchise, Dracula was defeated for good after a coalition of soldiers, religious orders, and the last Belmont killed him and sealed away Castlevania, the power that enabled him to keep reviving. It's possible for his reincarnation to become the new Dark Lord given the right circumstances since the reincarnation retains the powers and connection to Castlevania that Dracula possessed.
Done to excess in Tales of the Abyss. First, Luke's fonons are separating, meaning that he will die and no amount of life bottles or resurrection artes can bring him back, and then he stays behind after defeating a Load-Bearing Boss to use the Sword of Plot Advancement and either gets crushed among the rubble or goes up to the fon belt with Lorelei - there are two lights. Yet he shows up alive three years later with no explanation in The Stinger: happy ending, right? Wrong. According to Jade's character development sidequests, something called the Big Bang Effect means that since Asch's fonons entered Luke's body when Asch died, there's no way for even Jade to prevent Asch's mind overwriting Luke's, erasing his personality and leaving Asch with Luke's body and Luke's memories. Even though the game's mythology states that the souls of dead seventh fonists go to the fon belt with their fonons Luke won't even be able to reunite with Tear there: Asch will essentially eat his soul. It's no wonder that many fans of the game ignore that sidequest and say it's Luke based on the body language of people with every reason to think it is Luke - they weren't there for the sidequest and it is Luke's body, after all.
In The World Ends with You, the protagonist and almost all of the characters are Dead to Begin With; they're in a deadly game that they need to fight through to get a chance to be brought back to life. Failure means they get "Erased."
In Fallen London the dead can usually come back to life; this both applies to you and is referenced in-story. There are ways to bring permanent death, though: destroying (decapitating etc.) the victim's body, or the "Cantigaster venom". (Death from disease or old age is also final.)
In the Mortal Kombat games, the "Fatalities" each character can perform frequently conform to this trope. For example, one of Scorpion's fatalities in Mortal Kombat (also known as "MK 9") involves him slicing his enemy in half, then decapitating them, kicking the apparently lifeless corpse over... then slicing their severed head in half for good measure. However, such actions are also an example of Death Is Cheap, since they can be performed after every fight. Additionally, characters always seem to return in the sequels even if they've been disembowelled or completely destroyed in the past.
In Dragon Quest V, Pankraz the Hero/King is beaten to death on threat of child hostages, and then firebombed by the boss into a fine black powder. Comes off as Fridge Brilliance when you consider that resurrections in that game world are canon; When you get married the priest lampshades the fact that people can get resurrected most of the time, as to get around the "Until Death Does You Apart" clause.
Raziel from Legacy of Kain was already Undead before Kain had him executed. Now he's... really, REALLY Undead.
In Starcraft, Dark Templar energies are needed to kill the Zerg Cerebrates for good, since the Overmind would resurrect them otherwise.
In Skyrim, the Dragonborn is the only one who can permanently slay Dragons by absorbing their souls upon death which prevents Alduin from resurrecting them in new bodies. Possibly averted with Alduin himself, as rather than absorbing his soul after death his soul flies off into the skies, something that you can talk to Arngier about.
World of Warcraft used to have the rule that if a person was decapitated, they were permanently dead. However, the much-hated Creative Development team has now broken that rule so many times that it has become a joke.
Invoked in X-Men Legends II by Deadpool, who says he wants you "so dead you'd have to be reanimated as a corpse."
The Wizardry series, particularly in its earlier and most brutal games, could do this to you twice over. Run out of hit points or get hit by death effect, and a character is dead. If an attempt raise a dead character fails, or they're hit with a very powerful death effect, they're disintegrated to ash. If an attempt to raise a disintegrated character fails, or something truly extraordinary occurs (like teleporting into solid rock) they're "lost" and erased from your disk.
Later games were a little less brutal, introducing the "Extinct" status effect. It effectively meant "Deader Than Dead;" a character who was beyond resurrection. You could still look at the character sheet, though.
In Loom, characters can die, but if their soul is still nearby, they can be restored to life by way of the Healing draft. There also exists the draft on Unmaking, which is this trope as it completely annihilates the target in a spray of blood and organs, leaving nothing behind to resurrect.
In Mario & Luigi: Superstar Saga, you kill Big Bad Cackletta only about halfway through the game, but her spirit goes on to possesses Bowser, becoming "Bowletta". It isn't until the end of the game that you vanquish her for good.
In Super Smash Bros. Melee and Brawl, when characters are defeated, they simply revert back into their trophy forms and can be brought back to life with outside help. At the end of Melee's Adventure Mode, Bowser comes back as Giga Bowser this way, but defeating him a second time makes his trophy explode into dust.
A rather amusing example takes place in Metroid Prime 2. Throughout the course of the rather long battle against Chykka, the opponent is seemingly defeated in its larval form, but survives by rapidly aging itself into its adult form. Then, when it's defeated in that form, it's revived via Ing possession. When that finally gets taken out, its corpse remains in the area, which is fairly unusual for the series. However, if you scan it, the info basically goes out of its way to assure the player that this trope is in effect;
"Bioscan complete. Target Chykka has been terminated. Lifesigns are at flatline. No regenerative ability in effect. No evidence of symbiotic corpse possession. Resurrection does not appear likely."
Everybody who dies in 1/0 gets resurrected as a ghost sooner or later, leading to lines such as "Oh, quit being melodramatic. He's just dead." Max, however, loses his personality and gets transformed into an ordinary molecule, meaning by the established physics, he can't return at all. At least until Tailsteak lets the physics model break down at the end.
While characters never really come Back from the Dead in Dominic Deegan, Oracle For Hire (the key exception being Helixa and a handful of demons/ghosts), several have found themselves Deader than Dead in a fairly simple way - their souls were destroyed. This is not done lightly, however, as when a soul is destroyed it causes a massive explosion. The simultaneous destruction of thousands of souls at the end of the War in Hell rendered the landscape unrecognizable.
In Girl GeniusApplied Phlebotinum exists that can resurrect the dead and rebuild bodies that were burnt to a crisp. However, there's no way to rebuild a completely destroyed brain, and with an intact brain, resurrection just doesn't work sometimes. For this reason, some characters stay dead, and some don't.
In DMFA, after killing Dark Pegasus for the third time, Dan is seen enacting a sealing ritual: "No come back to life! No cookie!" (A much later comic cuts to his grave... and spends three motionless panels indicating that he's still dead.)
He does eventually come back. The very person responsible for it points out the minor flaw in Dan's approach here.
The undead race is made up of sentient zombies, brought back in order to have an unkillable horde, as they can lose limbs, organs, even be decapitated, and still put themselves back together. Unfortunately for their creator, they later ended up with free will and personalities of their own, so he devised a way of killing them off permanently that means magically frying them to ashes. As demonstrated on Hannah in Dan's flashback to his first adventure.
It is also revealed in the Demonology 101 pages that the undead can be killed permanently by having their brains destroyed.
In 8-Bit Theater, Sarda has killed the Light Warriors a dozen times, subsequently bringing them back so he'll be able to torture them some more.
However, the trope is played very straight with Black Belt. The author had his head chopped off and spraying blood to get people to shut up about bringing him back. Also, there never was a fifth Light Warrior.
And then there was the villain whose bones were broken and his skull buried upside-down at a crossroads. "Ideally, this is how we would dispose of all our enemies."
A black dragon attempted to do this to Vaarsuvius' children in revenge, by using necromancy to bind their souls and then leaving the earthly plane of existence. Even this would not have permanently killed them, but it would have removed them from Vaarsuvius's reach for all practical purposes.
When Kuboto just surrenders to Elan and explains that he will have no time to rig his trial and will stall things that will cause the heroes precious time, Vaarsuvius just casts a spell that turns him into a pile of ash. Followed by a wind spell that blows the ashes out on the sea. While there are still spells in D&D that can resurrect him, it requires extremely powerful allies and costs a fortune to perform.
Roy's father can't be brought back to life because he died of old age.
Similar to Kuboto, Malack and Nale are now Deader Than Dead due to their bodies being destroyed. Malack was a vampire, killed when Nale removed his sun protection spell, burning him to ash. In response, Tarquin killed Nale and Laurin disintegrated his body. She declared that if Malack can't be resurrected, nether will his killer.
While every player in Homestuck's Sburb has an extra life, it's still possible to be killed permanently if that life is destroyed. Still, one of the people killed this way has come back, so who knows? And besides, they still exist in afterlife in some form, from which they can be summoned if their remains are used to prototype a sprite.
Characters who die now get a special DEAD caption, just so that there's no confusion. And just to ram the point home, Hussie released this page, which is a who's who of who's dead.
In addition, Lord English has access to a powerful Breath Weapon that completely disintegrates anything it hits, up to the level of universes. His first on-screen use of it is on many afterlife characters, who are then... gone. Aranea implies that anyone hit by it is permanently obliterated. (With the possible exception of prototyping the remains of their physical/non-ghost bodies.)
In the Code Geass Abridgement, Code Ment, Young Lelouch and King Charles discuss Marianna vi Brittania's fate.
Young Lelouch: Dad! Dad! Mom is dead.
Emperor Charles: How dead?
Young Lelouch: Dead enough to cause Nunally to go blind.
Emperor Charles: That's pretty dead.
Most of the Forbidden Magic spells from Tal'Vorn fit this trope nicely. Specifically though; Dysjunction flings them so far out of this dimension that they certainly will not be coming back. They might not be dead, but they might as well be.
The Snap spell breaks every bone in the victims body to splinters. Which probably hurts.
CrimsonBranch had his face and most of his torso melted. Yet, he remains one of the most talked about characters in the fandom. Probably for a reason.
The Madness series seems to do this quite often as well, with many of the characters coming back to life in improbable ways, with the exception of the Sheriff, who after his death in Avenger, remains dead.
Poochie the Dog, from The Itchy & Scratchy ShowinThe Simpsons, is forcefully removed from that series quickly after his first appearance, and a lawyer shows up with a legal document that prevents him from ever returning, thus making him truly extremely dead. This being The Simpsons, he returns in a bunch of cameos anyway.
A Transformer can survive an insane amount of punishment, and many characters come back after being declared dead, or taking an amount of damage that really, really oughta do the job. The Chunky Salsa Rule is but a suggestion. (This isn't to say that Transformers never stay dead... but nobody ever knows what to make of a character's death. There's always someone else who went through worse and was just fine, or fixable, or rebuildable into a new toy, er, body.) However, there's one way to know one is truly done for, in-story: make sure that his spark, quite visible in a compartment in any Transformer's chest, is extinguished. (However, even then, there's Allspark energy...)
Even then, they just return to the Well of All Sparks (Transformer afterlife) where it's possible, if suicidally difficult, to bring them back. However, should something destroy the spark there (like being consumed by a dark god), then they are utterly erased from existence.
Even Optimus in Armada was brought back from being blown smithereens, supposedly via the Allspark.
Then resident Mad Scientist Wheeljack goes and creates the GT System in the backstory for Binaltech, which places the sparks in subspace (alongside Prime's trailer, presumably) where they operate their bodies by remote control...leave it to Wheeljack to make an immortal race even more immortal.
What's funny is, that is a needlessly complicated way of bringing back Prowl (died in The Movie, but made background cameos in some Japan-only series before Japan got the memo. So post-movie Prowl is a new body with the original Prowl's data - saved by Wheeljack - and animated by Chip Chase's soul until Prowl's spark can be recovered. Also, there are two Beast Wars toys named Prowl that don't resemble each other, so by way of retcon-fu, one Prowl is the fully revived G1 Prowl, and the other is an upgraded version of Chip/Prowl of "two-second Transformers Headmasters cameo" fame. Interestingly, the latter Prowl's packaging, written before the Binaltech retcon, gives him a bio that gives him a very G1 Prowl personality, and says he is convinced he was a great strategist in a past life, suggesting that he is a new Prowl who is a reincarnation of the old one - easily possible since sparks can be retrieved. So maybe we can call TF the ultimate aversion of Deader than Dead — kill a character and mean for it to stick, and you'll find he gets resurrected twice, and may live yet another life later.)
Compared to that, Ravage's feats of Deader than Dead survival seem unimpressive. However, Ravage is in an exploding ship in Beast Wars, and we see his head kicked knocked off a cliff later - the writers assuring us that he's not "five minutes in a CR Chamber" dead, but really, seriously Killed Off for Real dead. Three different comic series have found different ways of bring him back.
Another way to terminate a Transformer with extreme prejudice? Rip out its spine and use the barely-recognizable carcass to whack another enemy over the head. That's the aforementioned kitty's fate in the Transformers Film Series. And in the movieverse, Death Is Cheap is averted; so far, everyone who looked dead was dead if you didn't apply Allspark energy. But no, Ravage lives on in the comics (though his death and mysterious return were acknowledged, and Soundwave can't sense him anymore, meaning it's less Unexplained Recovery and more "someone/something brought him back but not as he was before.") But in all these cases, the original writer wanted the characters capital-D Dead, took steps to show us that yes, this is death-death and not "Waspinator kablooification of the week..." and underestimated the ability of writers to follow to easily think of a way around it. The First Law of Resurrection will not be denied.
In Jonny Quest: The Real Adventures, the season 2 writing staff wanted to bring back themes and villains from the original show, and thus decided to kill off all recurring villains from the previous series. One of said villains was Ezekiel Rage, who repeatedly came back from No One Could Survive That situations. So what did said writing staff do? Send him back to the prehistoric era with a nuke that explodes and show his skull mask being found in the present day just to drive it in.
The Nibiru Entity from Scooby-Doo! Mystery Incorporated was destroyed so utterly that it was completely erased from existance, present, future and past. This led to history being changed so that all the atrocities the creature had orchestrated over the centuries never happened, leaving the gang (and Harlan Ellison) as the only ones who still remember the original timeline.
Pseudo-Demetrius I, a Russian adventurer who claimed to be the last heir of the Rurikid dynasty who came Back from the Dead and (for a while) was accepted as such. When they exposed him as a fraud, they executed him, burned the remains, put the ashes in a cannon and shot them away. Didn't help, another Pseudo-Demetrius appeared after a while, claiming to be Back from the Dead again. This time, the Russian Orthodox Church found a more permanent solution: canonizing the real Demetrius as a saint and threatening to burn anyone pretending to be him as a heretic. This time it worked.
Information-theoretic death, defined loosely as "so dead that not even hypothetical future technology can bring you back". This is as opposed to clinical death, which is defined as a lack of breathing or heartbeat, and can and has been reversed.
According to some theories, falling into a black hole would result in this.