A container or object which holds all or part of a person's soul (or life, or heart) outside of their body; this makes that person immortal and/or invulnerable. The only flaw is that the Soul Jar is now their Achilles' Heel. Usually, they make sure it is very well protected (the word phylactery, the common name for this kind of container from Dungeons & Dragons fame, actually comes from Ancient Greek phylacterion, form of phylássein, (φυλάσσειν) meaning "to guard, protect").
Typically, Soul Jars work in one of two ways:
1) The person whose soul is jarred cannot be physically killed (or in some cases even injured) as long as the jar is intact. This one has two sub-categories:
1a) Destroying the jar kills the entity whose soul was jarred. (See the Yura of the Hair example below)
2) The person can be physically killed while the jar is intact, but they simply come back with a fresh body, in which case it doubles as a form of Resurrective Immortality. They can only be completely killed by first destroying the jar, then killing their current body. (Voldemort's horcruxes are of this type.)
Durarara!!: Although Celty lives separately from her head, she worries that if it's destroyed, it might also kill her. Whether or not that's actually true has yet to be seen, but trying to kill her the normal way definitely doesn't work.
Naraku, Big Bad in the series InuYasha, treats InuYasha as little more than an annoyance early in the series. However, as InuYasha gains power and becomes a real threat, Naraku — who is an amalgamation of hundreds of demons — splits off his heart in the form of an infant, which he hides away under the protection of another of his incarnations, making him effectively immortal. The Soul Jar actually decides to take advantage of this and tries to kill him with a super-powerful demon he made. This backfires, as Naraku reabsorbs him and his henchmen so he is no longer immortal, he'll just have to be satisfied with having a body made of diamond and harder-then-diamond plates.
Likewise, Yura of the Hair, the first enemy that InuYasha and Kagome fight after their quest begins, has hidden her soul in a comb. None of the horrible wounds InuYasha inflicts on her are more than a mild inconvenience — until Kagome destroys the comb (which Yura inexplicably led her to), at which point she dissolves.
In 3×3 Eyes, a "Wu" is the formerly-human servant of a member of the mystical, three-eyed Sanjiyan race. The Sanjiyan holds onto the Wu's soul, meaning that, as long as the Sanjiyan survives, the Wu will just regenerate from all damage. The main character Yakumo Fujii is a newly created Wu, bonded to the Sanjiyan Pai, and he learns just how immortal he is the hard way — many, many times. To the point where the series could be summarized as "Yakumo is coughing up blood AGAIN."
The requisite Wham for Code Geass R2 episode 20 reveals that one character ( Empress Marianne) had cheated death by turning another one ( Anya Alstreim) into a living, breathing Soul Jar.
Slayers Next has the Pledge Stone, a contract between a human and a Mazoku. As long as the Pledge Stone is intact the human is immortal.
Try has a more literal interpretation of this trope; one episode revolves around Lina and Filia being stuck on a haunted ship created to torment a man named Jarlov, whose soul is trapped in an actual jar.
Revolution and Evolution-R have Rezo the Red Priest return via a soul jar, as well as Naga the Serpent, whose soul has somehow been removed from her body by a malfunctioning soul jar and then given form in a suit of animate armour. This time the Soul Jars are, again, really jars.
One character Julian is a god's Soul Jar ( Poseidon) in Saint Seiya.
In the OAV, it happens again. Same two characters.
Similarly, and to everyone's dismay, a main character ( Shun) was used as a Soul Jar for a different god ( Hades) by Pandora since infancy.
Yugi Mutou in Yu-Gi-Oh! is the wielder of the Millennium Puzzle and is the living Soul Jar for his other personality ("Dark Yugi", "King of Games" Pharoah Atem's spirit). Likewise, Ryou Bakura is a living Soul Jar for his own alternate personality from the Millennium Ring (Dark Bakura, spirit of Thief King Bakura). Dark Bakura himself specializes in producing Soul Jars with his Millennium Ring in order to spread his power as needed, and is ultimately revealed to be a Soul Jar himself (for Zorc).
In the Duelist Kingdom arc, Pegasus J. Crawford uses a version of this as a Penalty Game by transferring Sugoroku Mutou's, Mokuba's and Kaiba's souls into inanimate objects. Sugoroku's Soul Jar was a video tape and the Kaiba brothers' Soul Jars were blank playing cards known as 'Soul Prisons' (in the anime, all three were put into Soul Prison cards because Card Games). By doing so, the trapped characters lose all personality and appear to be within a catatonic state. It is unknown completely what happens if the inanimate objects are destroyed or damaged in some way, but it is generally acknowledged that it can't be good.
In the sixth volume of the original manga, there is a one-shot villain who finds a cursed card game called Dragon Cards that seals the loser's soul in a jar. He steals the Millennium Puzzle from Yugi and forces him into a battle. Yugi loses, but manages to get his hands on the puzzle before losing his soul, and Dark Yugi is able to come out and win a rematch.
Alucard's coffin is implied to act as this for him. He appears to require a certain proximity to it in order to access his higher powers (as evidenced by his needing to take it with him on missions where he is expected to use his greater powers), and it appears to be an extension of himself in some manner (such as when it sprouted limbs and eyes during Hellsing: The Dawn and carried him away from battle when he came under threat). He is also highly protective of it. Plus, it contains his army of familiars, which are the basis of his Nigh-Invulnerability; as long as they are in the coffin, he possesses their collective life force making him extremely difficult to kill, and even when they are out of it he can defer his own injuries to them (at the cost of gradually destroying them). Whether this is the case for all higher level vampires or was a part of the measures Hellsing initiated in order to keep him under control is unclear.
The titular cyborgs from the Neon Genesis Evangelion verse are similar to a Soul Jar. It is directly confirmed that at least two hold the mothers of their respective pilots. These souls differ somewhat: Yui got stuck in Unit 01 due to a contact experiment where she reached a 400% sync ratio; due to that, she's in complete control and can interact with the outside world to some extent. Kyoko had gone through a glitched version: Unit 02 took the part of her which recognizes Asuka as her daughter, leaving the rest suicidally insane. Unit 00 is a source of argument among fans. The most common theory being that Rei I is inside. To some extent, the Reiqarium might apply as well. In the event that Rei dies, her soul will go to the chamber and possess one of her clones.
In Naruto, Kakuzu collects people's hearts and incorporates them into his body. He can also use them to animate minions for him. Whether they are inside or outside his body, he can't die unless they are all destroyed.
The Curse Marks that Orochimaru bestows on certain people actually carry his will, meaning that he can be potentially reborn from the seal of anyone he has given one to.
A Deoxys's chest-located crystalline core is a perfect example, possibly. This is especially prominent when a Deoxys rebuilds itself from the core being the only part left over after being vaporized into white sparks by a Rayquaza's point blank Hyper Beam in one of the movies. The core was not vaporized along the body, and how durable it is is a mystery.
Witches hatch from their Grief Seed, and they leave it behind when they are killed. Magical girls use the Grief Seeds from defeated witches to recharge their powers, although it's stated that too much use of a Grief Seed can revive the witch. Which is why Kyubey eats "used-up" Grief Seeds.
Later, we find that a magical girl's 'Soul Gem' is an entirely literal name — upon making the contract with Kyubey, a magical girl's soul is placed inside the gem, which becomes her new "body" which controls her original one, which essentially turns her into a lich. It can be used to affect her original body by means of stimulating it (a fact that the fandom has run away with). It cannot be more than 100 metres from its owner or else the original body will lose consciousness and enter an Empty Shell state until the Soul Gem is brought back — and if the body goes too long without the gem, it starts to decompose just like a corpse. Finally, as long as the gem is intact, the magical girl will eventually recover from any wounds her original body takes, but if the gem is ever destroyed, as happens several times in the series, the magical girl will immediately — and irrevocably — die. Much later, we find out that Soul Gems will eventually become Grief Seeds, and Magical Girls will eventually become Witches.
Karla, the Grey Witch in Record of Lodoss War. Her soul is actually housed in a circlet with two red eyes embedded in it. The exact circumstances by which she ended up in this state are unclear, but she can possess anyone wearing the circlet, and she does seem able to move alone to some limited degree so as to possess someone else, such as when she was forced off Leylia and had to switch over to Woodchuck. In the manga, Karla's circlet is apparently unable to move at all. Woodchuck takes up the circlet willingly out of self-loathing.
Type-Moon example: Zouken Matou is a worm-user whose body is made completely of (you guessed it) worms. So long as he keeps his worms fed and the master worm containing his soul is safe, killing his apparent body does nothing, as it can be replaced with more worms, though by this time in Fate/stay night his magic is reaching its limit, and he will eventually be unable to sustain the amount of humans he needs to consume to stay alive. His mind and soul have also decayed to the point where he doesn't even remember why he wants to be immortal.
Omamori Himari: Lizlet's teacup is her true body. The "human" one is effectively indestructible, as well as incredibly strong.
The titular violin in the Total Drama story, Courtney and the Violin of Despair houses the embittered spirit of a former owner. Although that former owner’s body is long since dust, the spirit remains and enforces the curse on the violin. Destroying the violin enables the spirit to rest in peace.
In The Commander Of Shepherds, Celestia and Luna will regenerate from the Sun or the Moon respectively, as these are the sources of their power. The same is true for Twilight and the Element of Magic - Word of God goes as far as calling her a lich.
The mane 6 statuettes from Fallout: Equestria, although all 42 of those figurines are actually all made from Rarity's soul alone.
Death Note Equestria eventually reveals that Pinkie Pie managed to do this prior to her death... with a bag of potato chips.
Films — Animated
Anastasia: Rasputin sells his soul to the underworld in return for the demonic powers to enact his curse on the Romanov family. His body can still die, but he just ends up undead in limbo. He can only move into the afterlife if his curse is complete. What's bizarre about this, is he literally sold his soul for the MacGuffin. If his reliquary is destroyed, he ceases to exist. Trying to analyse this, or explain how a person's soul can be both simultaneously transplanted and substituted, for something that's not a soul, causes an ontological nightmare.
In All Dogs Go to Heaven, a person's life is measured by a timepiece. Charlie steals his after death and winds it back up again, returning to life. This has the downside of meaning he'll go to Hell when he finally kicks it again, but he's not too concerned, since as long as the watch keeps ticking he's effectively immortal.
The Stitchpunks in 9 are animate and almost literal example.
Films — Live-Action
In Dragonslayer, the hero's mentor places his spirit (and, apparently, also his body) in a magic amulet that enables the holder to make use of magic to a degree. He does this so that his young apprentice can do the travelling for him.
In the third film, it's revealed that putting your heart in the chest is actually a requirement for being captain of the Flying Dutchman. The captain certainly needs the immortality to be able to seek out and ferry the souls of the dead to the afterlife.
Jones probably started the tradition — the real reason he tore out his heart and put it in the chest was that so he wouldn't have to feel anymore, because he was supposed to ferry the souls of the dead for ten years and then be released when he returned to his lover; when his lover wasn't there, dooming him to at least ten more years and possibly eternity until his own death, he was so heartbroken he did the heart thing. The immortality was probably an unforeseen side effect, although now any poor schlub who takes the job has to do it.
And for a while it actually was in a jar. A jar of dirt, to be exact.
In the 1974 film Phantom of the Paradise (which is a fusion pastiche of Dorian Gray, The Phantom of the Opera, Faust and several other stories), evil record producer/promoter Swan (played by Paul Williams) keeps a videotape of himself making a Deal with the Devil; his image on the tape ages, but he does not. The tape also represents the physical contract of that deal; both he and the titular Phantom (whom he tricks into making a deal of his own) are immortal while their contracts are intact.
This is pretty much the whole point of the film Cold Souls. Paul Giamatti (played by himself) stores his soul in a literal jar in order to play Uncle Vanya. Hilarity Ensues.
Putting the souls of their dead in a jar is apparently SOP for Vulcans.
In Dragonheart Draco serves as Einon's soul jar. By Draco giving him part of his heart, Einon regenerates all wounds he suffers unless Draco himself is killed.
Horcruxes in the Harry Potter series serve as this; pieces of the user's soul stored in objects of some kind.
J R Ward's Black Dagger Brotherhood is a good example: when the Omega creates a lesser, the heart is removed and placed in a ceramic jar. For some reason, the brotherhood attempts to find and store these each time a lesser is killed.
In Oscar Wilde's The Picture of Dorian Gray, Dorian Gray's wish for eternal youth is granted. His portrait, which has just been painted, starts to age instead. Has a twist, in that rather than being defeated by a hero who discovers the source of his immortality, Dorian fends off all threats but is eventually destroyed by his own self-loathing. The twist was discarded for the oft-maligned movie version of The League of Extraordinary Gentlemen; in the film, Dorian Gray is forbidden to ever look at the painting as part of his end of the deal... and of course, in the end it's used to kill him.
In PC Hodgell's Chronicles of the Kencyrath, some members of the not-quite-human Kencyr have the ability to hold onto another's soul for a time. The one without a soul is nearly immortal, but lacks a conscience and casts no shadow. The one carrying an extra soul casts two shadows.
From Harry Potter, there's Voldemort's six Horcruxes, although these only hold one-seventh each of his soul (six Horcruxes plus one Voldemort). Things started to go wrong when Voldemort accidentally made Harry into the sixth Horcrux. (Voldemort had made five by then, and he would make a seventh about thirteen years later.) As a result of all this soul-splitting, toward the end of the series he becomes noticeably unhinged. Another complication is that the Horcruxes only protect Voldemort's spiritual existence. He can still be killed physically, which would require him to be revived by someone else. Lastly, to an extent the Horcruxes are able to act independently, though all of them look for the same as their original vessel. This incidentally is one of the reasons Harry was able to return from the border between life and death after Voldemort hit him with the Killing Curse again. Voldemort's own soul fragment was in the way, sparing Harry the full brunt of the curse.
The Tales of Beedle the Bard gives us "The Warlock's Hairy Heart". A young warlock cuts out his own heart and stores it in a case so he might not ever feel such pesky things as emotion, rather than immortality.
In the book and series Neverwhere, the Marquis de Carabas keeps "a piece of his life" in a box in case he is ever killed. He is.
Subverted in that it's used as a punishment in the Wheel of Time series. Moridin currently holds two of these from members of the Forsaken that really screwed up.
Fritz Leiber's Fafhrd and the Gray Mouser series featured one villainous sorcerer who took his soul and hid it in an egg in a magical castle.
Lifetimers in the Discworld. In Soul Music, Albert carries his around with him while searching around in the world for the missing Death - a mistake, as he gets mugged and the hourglass shatters. Fortunately, Death manages to save thirty-eight seconds' worth of time and pour it into a bottle to prevent Albert from dying (again).
And there's a reverse example in Hogfather, where the Hogfather's lifetimer shatters in response to Teatime's plan to stop children believing in him, thus "killing" him.
Also, in Carpe Jugulum the heart in a hidden jar variation is mentioned to be used by magicians in Howondaland so they can't be killed.
The One Ring in J. R. R. Tolkien's The Lord of the Rings. It wasn't actually created for this purpose — the Dark Lord Sauron was already an immortal spirit able to take any form he wished, and created it as an Amplifier Artifact that would make his already formidable Mind Control powers strong enough to take over the other Rings (and through them, their wearers). But upon creating it he put part of his Life Force into the Ring, which kept him from dying completely when he was killed as long as the Ring survives. Morgoth did the same thing with the entire physical universe. Every last atom contains a minuscule fragment of his spirit. Hence why evil endures even though Morgoth was thrust out into the Outer Dark by the Valar: "the whole world is Morgoth's Ring."
In the Apprentice Adept series, the harmonica Stile first summons to use for his magic turns out to be the one created by his doppelganger, Adept Blue. We find out later, it stores Blue's soul (Blue arranged to put his soul there after allowing Red's booby trapped amulet to strangle him). Later still, Adept Brown builds a flesh golem for Blue's soul to inhabit... which Stile ends up in at the end of the Phaze/Photon-saving scheme (Don't worry, this is actually a good thing).
In Barry Hughart's Chinese fantasy novel Bridge of Birds, the Duke of Ch'in (a pastiche of the historical Qin Shihuangdi) is revealed to have had his heart removed by the wisest man in the world, who implies that he was the one who did the same to Koschei the Deathless.
In The Riftwar Cycle, Leso Varen has one. In a moment of Lampshade Hanging, Pug remarks that it could be any object, not just a jar; it turns out to be a jar. In subsequent books, it is revealed that Varen has multiple Soul Jars in a number of locations across Midkemia and Kelewan.
In John Barnes's One for the Morning Glory, they deduce that Waldo must have done this by the magical powers he gains from it; with the aid of the Riddling Beast, they track it down and destroy it.
In the "Boy Who Couldn't Die", an evil monster puts its own soul into a "jar" and becomes effectively immortal. The main character seeks to duplicate this.
In Mistborn, the Lord Ruler's bracers hold his youth and vitality, making him into an immortal Implacable Man. These are an interesting example, though, as they must be in physical contact with him at all times for him to benefit from the stored energy. When Vin yanks them off during the final battle, the Lord Ruler instantly collapses and begins to age into a withered old man. He's dead in minutes.
Inheritance Cycle pulls this out near the end of the third book, where it's revealed that dragons can live forever if they cough up an internal gemstone for someone else to hold. If the dragon's physical body is killed, their soul is transferred to the gemstone. Unfortunately, those gemstones are a source of great magical power and a favorite collectable for bad guys to hoard. They also don't actually increase the lifespan of the dragon; the soul is simply transferred upon death (while the dragon seems to be put in a state of virtually absolute isolation and impotence).
In The Death Gate Cycle, Haplo manages to expel his soul from his body and turn it into a dog - entirely by accident. There's probably some deep philosophical implication to the fact that whenever Haplo neglected his soul for too long, it would sneak off and pilfer sausages, but it was never investigated within the story.
Demons in Fred Saberhagen's Empire of the East and Books Of Swords universe suffer from this. That is, their "lives" are bound to an inanimate object. While there are other ways of killing them, destroying their lives requires no special skill and is by far the easiest.
In the Secret Histories series by Simon R. Green, it is customary for witches to magically separate their hearts from their bodies and hide them in order to make themselves very hard to kill. The spell can also be applied to someone else without their knowledge.
In Howl's Moving Castle (the original book), two characters have made deals with fire demons wherein the fire demon gets the mortal's heart, letting the fire demon live, and greatly extending the mortal's life and giving them access to the fire demon's power. This ties the two together (one dies, both die), so it's not as useful as a normal Soul Jar, but the heart does act as a Soul Jar, in that you destroy it, you destroy them.
The painting of Queen Etheldredda in Septimus Heap, while not being a literal Soul Jar, serves this purpose for her and its destruction in the BoneFyre causes her ghost to disappear.
The Book of Lost Things has a literal example; the Crooked Man's life is sustained via the soul of a child that he keeps in a jar.
Tales of Kolmar has the Demonlord survive via the spell of the Distant Heart. His heart was removed, turned to stone, and hidden under a mountain by demons. His soul went to the demons. As long as heart, body, and soul were not all in one he couldn't really be killed, and even then only by something that had dragon and human blood both.
There's also the soulgems of dragons. They each have a gem in their forehead; after death it's collected and a Kin-Summoner can make them glow steadily and call the deceased back to speak through them for a time, but otherwise the dragons are truly dead and believed to have some kind of afterlife. Soulgems of the Lost, those struck down by the Demonlord, can't be used to summon and flicker with a faint and constant light. When they're restored in Redeeming the Lost we see that [[spoiler: some of them were asleep, some came in and out of consciousness, some were awake the whole time.
There's a somewhat unusual example in Sabriel, first book of the Old Kingdom series. Kerrigor uses his original mortal body as his anchor in the world of the living (he usually exists either as pure spirit or uses a magically created vessel), and so long as it exists he can never fully be banished from the world. Subverting expectations, it's also never destroyed; Kerrigor retakes his body at the climax in order to keep Sabriel from destroying it, and is shortly after bound to eternal slumber while still inside it.
Live Action TV
Babylon 5 had Soul Hunters, beings who sought to preserve knowledge and wisdom by capturing and maintaining the souls of the dying. This causes serious issues with the Minbari, who believe that their souls are reincarnated in the bodies of later generations of Minbari (and there is some evidence—although not perfect evidence—to believe that this is literally true), and that the Soul Hunters' preservation process prevents that reincarnation.
In the TV show based on Jim Butcher's The Dresden Files series, a condemned wizard known as Bob is imprisoned in his own skull after performing magic to raise the dead. In the original books, he's an air spirit bound to a skull.
In an episode of Angel, a vampire has his heart surgically removed so that Angel can't stake him. Unusually for this trope, he is eventually defeated not by locating and destroying his heart, but by waiting until the time limit was up.
There's also the literal jar where Angel's soul was sealed to bring Angelus out temporarily.
In Angel & Faith: Angel is using himself as a Soul Jar for pieces of Giles' soul, as a prelude to resurrecting him.
In Tin Man, Azkedellia attempts to pass off an artifact to DG as one of these, complete with their mother's voice calling out for DG. Subverted in that DG doesn't buy it for a second and smashes it to bits, using the resulting distraction to try and escape.
In the relaunched Doctor Who TV series there are a number of episodes in the third season featuring a "Chameleon Arch", a Time Lord device that rewrites biology and can be used to disguise a Time Lord as a human. In the process their mind, memories and "Time Lord essence" (re: glowy swirly energy stuff) are hidden in a pocket watch for safekeeping. The Doctor used one to escape some enemies who were chasing him through time by disguising himself as a human school teacher just before the outbreak of the First World War; the bad guys' attempts to find the pocket watch containing the Doctor's "soul" for their own nefarious purposes drives the plot. the Master also uses one of these to disguise himself as a human at the end of the universe to escape the Time War that destroyed the Time Lords. Subverted in one of the later specials, where the Doctor meets a man suffering from amnesia who he thinks might be his own future self under the effect of a Chameleon Arch but his pocket watch turns out to be just an ordinary pocket watch and he is actually just a human with alien-induced amnesia after all.
The Star Trek: The Original Series episode "Return to Tomorrow" had some of these in which the alien survivors of an apocalyptic war remained, and then swapped consciousnesses with members of the Enterprise crew, trapping Kirk and Spock in the jars.
Star Trek: Voyager has an interesting case with The Doctor and his mobile emitter. As a hologram, he is physically invulnerable, so villains must therefore target the mobile emitter he wears on his arm in order to exist outside of sickbay/holodeck. Stealing or deactivating it is a common way to incapacitate him.
Some of the artifacts in Warehouse 13 contain more of their original owner's personality than others, most notably Lucrezcia Borgia's hair comb, which channels Lucrezcia's personality, desires, and her gifts of influence into its wearer.
The warehouse has the actual looking glass of Through the Looking-Glass. The murderous spirit of Alice Liddel is contained within.
H.G. Wells also gets this treatment. Her mind is trapped in a coin while her body keeps going with a false personality running it.
The hard drives holding personalities in Dollhouse might qualify.
In Once Upon a Time, several sorcerers are able to remove people's hearts and keep them. They can use the hearts to control their owners or crush them to kill them instantly. Also, one of the main characters has removed her own heart and keeps it in a concealed box.
A Mi'kmaq Native American myth about a dispute between the god Glooskap and a giant who had hidden his soul in a pinecone, and hidden that on the top of an unclimbable mountain.
The example given in Literature, from Fafhrd and the Gray Mouser, is taken from an Indian myth. This story (and others like it) arguably form the ur-examples of the concept of the Lich in popular culture (see the D&D examples and others, below).
This can also be done in limited fashion as early as 1st Edition using the magic jar spell. The caster enters a gem or whatever, then swaps with (possesses) someone in range.
AD&D 2 Al-Qadim ("City of Delights") has "Hide Heart" spell, which allowed the hide-your-heart-in-a-jar stunt for partial immortality... and if cast on someone else, ensures they not only are more likely survive the mission, but will want to return.
1E adventure C1 The Hidden Shrine of Tamoachan. In one room there was a werejaguar who could turn into a statue at will. His heart had been removed and stored in the head of a stuffed tiger nearby. He will apparently die if he takes enough damage, but will be reborn in one day's time unless his heart is destroyed.
The 1E adventure I3 Pharaoh had an Evil high priest named Munafik who magically removed his heart and stored it in a glass jar. The only way to kill him was to destroy the heart.
"Heart of Stone" from Player's Options, where the heart is replaced with a stone duplicate, turning the caster for a year into not-quite-living being, resistant to any weapons but having problems with healing. Codifies what was done years earlier by the Big Bad in an Expert D&D module The Curse Of Xanathon.
3rd Edition includes the "Hide Life" spell, which has much the same effects, but is written to duplicate the Prydain variant.
Amulet of Life Protection — stored the user's soul for a week after death to ease the resurrection, protected from magic jar and suchlike. Locket of the Great Kingdom from Greyhawk did much the same, but the dead user could use magic jar and raise an easily possessable basic mindless undead.
Powerful spellcasters can undergo a dark ritual to become mighty undead known as Liches by storing their soul in a phylactery. If their body is destroyed but the phylactery isn't, they eventually reanimate. Well-illustrated in the D&D parody webcomic The Order of the Stick, where the Big Bad, Xykon, is a pretty standard lich who does indeed regenerate from a phylactery — body part by body part over quite a few strips. A more advanced and ancient form of liches exist known as demiliches, whose bodies have disintegrated away to a single part of the skeleton (usually a hand or skull) embedded with "soul gems" that give them additional powers. Both the phylactery and the soul gems must be destroyed to keep the lich dead, though the latter is fairly trivial. In some sources the Demilich itself is said to be a Soul Jar, the actual lich having evolved into a spirit that spends most of its time on the Astral Plane; it's just a Soul Jar that wakes up and kills you if you mess with it.
Among Ravenloft darklords, Soul Jars are possessed not only by Azalin the lich, but also Stezen D'Polarno, whose soul is bound to a painting, and Hazlik, whose Soul Jar works like a Horcrux. They're not the only darklords who won't stay dead easily, mind: they're just ones who happen to use Jars to come back. In some cases, a Ravenloft domain is, itself, a Soul Jar for its darklord.
Forgotten Realmssourcebooks and novels featured a few spellcasting or magic-manipulating items powered by the trapped spirits of wizards. So a Wizard Wand doesn't just release pre-set charges on a command until it's dry, it can memorize (after a rest) spells from a spellbook or a scroll to cast when requested, at the trapped wizard's level. Magisters upon death or retirement (usually it's the same) may choose to have their spirits placed into magic items, turning these into borderline artefacts.
GURPS 4th Edition has three variants of this: Soul Stones, which make the wizard immortal so long as the stone is intact; Soul Jars, which allow the wizard to move their consciousness to the jar if their body dies, and Soul Golem, which allows the wizard to put their soul into the body of a magical Humongous Mecha. Note that these Soul Jars consist a "2b" version of the trope: killing the jarred character does destroy their body, and they can't automatically come back. However, the Soul Jar does house their spirit, leaving open the possibility that they or someone else can use another power to bring them back.
Vampire: The Masquerade allows a character with five dots in Serpentis to perform a ritual to remove and conceal their heart, becoming unstakeable. With eight dots and Clanbook Followers of Set, you can do this to someone else and hold their heart for ransom.
In Legend of the Five Rings, the Bloodspeaker Iuchiban achieved immortality by cutting out his own heart and hiding it away in a box, but is eventually defeated when Isawa Sezaru destroys the heart. Later, a servant of Big Bad Daigotsu was forced to undergo the same procedure. This "Ceremony of the Hidden Heart" was originally developed by foreign sorcerers of the Burning Sands. The big drawback is, of course, that if someone gets a hold of your heart-box they can kill you as easily as they would cut up a steak. A great deal of the intrigue in the city of Medinat al-Salaam involved finding, stealing, or destroying these hidden hearts.
In Warhammer 40,000 the Eldar race carry Soul Stones on their persons, to avoid their Souls being consumed by Slannesh, the Great Devourer, upon their deaths. These Soul Stones are then transferred to the Infinity Circuit upon the death of the eldar carrying it where their soul is released. To help, among other things, guide the younger eldar, and power their Craftworld. In times of great need these Souls can be called back from the Infinity Circuit and places into man-sized or huge constructs known as Wraith Guard and Wraith Lords respectively. The construct bodies can be destroyed but as long as the Soul Stone is intact, so is the soul. The Necron consist of an entire army of soul jars, each Necron unit containing the soul of a Necron. Unfortunately, that means every time a Necron is damaged and repaired it loses a fragment of its soul.
In Warmachine, the Cryx Empire is able to make Soul Cages. The Iron Liche, Asyphyxious actually cages his own soul, and replaces all but his Skull with a steam and magic powered body. As long as his Soul Cage is intact, he is not really dead.
Platinum Angel is a Type 1b Soul Jar, albeit a very vulnerable one (she is both an artifact and a creature, and every single color in the game have a method of destroying one or the other fairly easily). Abyssal Persecutor is the inverse of Platinum Angel, in that it's effectively a Soul Jar for your opponent as a way to counter the card's otherwise excessive strengths. Since Persecutor is so powerful, it will likely become a Type 1a Soul Jar very quickly, forcing your opponent to protect your card just to ensure his survival. Playing both cards means the game is effectively halted until one of them dies.
In the Conan the Barbarian RPG, one of the abilities available to the Sorcerer class is the Picture of Corruption, and it's basically one great big Shout-Out to The Picture of Dorian Gray. The picture takes damage and "Corruption" for the sorcerer, but the sorcerer constantly has to check the picture. If it's destroyed, they immediately age to however old they ought to be, and take all the damage stored in the painting.
The Monstrance of Celestial Portion in Exalted is a variant on the concept. If a deathknight is killed, his Exaltation - the part that makes him an Exalt - returns to the Monstrance, from which it can be transferred to a new mortal host chosen by the deathknight's master. Without the Monstrance, the shard would wander freely and choose its new host itself. Destroying the Monstrance won't kill the deathknight, but instead free him from his master's control; the trick is that not all of them know this, and may believe it would kill them.
The fetich souls of Primordials also serve as a form of this. The fetich embodies the identity of the Primordial; should it be killed, the Primordial will undergo a major redefinition, which may wind up creating an entity who is entirely different (for all intents and purposes killing the original). Fetich death was feared by the Primordials as the only way of "killing" them (even though another being with certain of their traits will result) until the Solars came along and developed powers that could actually kill them (which, incidentally, had nothing to do with their fetiches).
In the first edition of Exalted, there is also a Solar circle spell which uses a complicated ritual to allow a powerful Exalted sorcerer to store his soul in an artifact.
Call of Cthulhu campaign Shadows of Yog-Sothoth, adventure "Devil's Canyon". The spectral hunters cannot move than 1 mile away from their kachina dolls, which hold their souls. If a specific chant is conducted over a spectral hunter's doll, it is destroyed.
One of the gruagach Virtues is External Soul, which allows the user to extract his soul from his body and place it in an object, which is then placed in a safe place. While this is in effect they cannot be killed unless the object is destroyed first.
The giants known as famhairan a'falach are the original source of gruagachan magic. They can remove their hearts (which contain their souls) from their chests and hide them in a safe place, with the same benefit as above (can't be killed unless the heart is destroyed).
Everway supplement Spherewalker Sourcebook. The Red Merchants have their souls removed by their ruler, Queen Sunset the Undying, and placed in a receptacle. This basically causes them to become a form of vampire: immune to aging and vulnerable to only certain types of harm.
Witch Hunter: The Invisible World.
The Bennu Sacrament rite allows a sorcerer to have his heart removed and stored in a canopic jar. This makes the sorcerer immune to poison, fatigue, blood loss and most diseases, and grants high resistance to weapons and other physical traumas. If his body is destroyed by fire or chopped into bits it will eventually regenerate. If the heart is taken from the jar or damaged in any way the sorcerer dies.
The Mystical Price called Soul Outside causes a creature to have a vital part of its soul stored in another location. The soul part must be kept in a container. If it is ever destroyed, the creature is completely vanquished and may not return.
The Kanohi Ignika, Mask of Life in BIONICLE, when Physical God Mata Nui's spirit was forced into it, and again later, when Mata Nui willingly put his own spirit into the mask for safekeeping and, well, because he wanted to keep himself out of the world's happenings.
The Dark Elf in Final Fantasy IV was doing this with the Crystal of Earth. As long as the Crystal is on his pedestal and not the usual one, he could regenerate. (He comes back again in The After Years.)
Played perfectly straight and possibly the Trope Namer in Might and Magic 7, 8, and 9, where necromancers and evil wizards actually need an item called a Soul Jar to contain their souls and transform into Liches. Notably, in 8 the Soul Jar is implied to be temporary. You put the soul back into the person after the transformation. Corak's Soul in Might and Magic 2 qualifies as well.
In Diablo II, the only way to ensure that the Prime Evils never return to the mortal world is to destroy their Soulstones. Of course, the only reason the Soulstones exist to begin with is because the Evils somehow convinced the world that using them would do this. Bad Evils! Or, if Izual is to be believed, it's actually a gambit on the part of good manipulating evil, not evil manipulating good. The original plan was to imprison the Evils in the Soulstones so that they would not return to Hell upon death. But Izual betrayed Heaven by filling in the Evils on how to corrupt the Soulstones and helped the Prime Evils mastermind their own exile into Sanctuary, setting up the events of the series proper.
In Diablo III, the Black Soulstone becomes the Soul Jar of all seven Prime Evils thus making it the Soul Jar of the original Prime Evil Tathamet.
In Paper Mario, the boss Tubba Blubba was made invincible by removing his heart and hiding it. Mario finds the heart and tries to destroy it, only to prompt Tubba to reunite with his heart... which costs him his invincibility, and allows Mario to (very easily) defeat him.
In the Baldur's Gate 2's expansion Throne of Bhaal, one of the main antagonist, the Fire Giant Yaga-Shura, is made invincible by a ritual removing his heart and protecting it.
The Warlock class from World of Warcraft can create "Soul Stones" that store the target's soul, granting them an instantaneous resurrection should they be killed while the buff is in place. They can only be made if you have "Soul Shards," which is basically the extracted soul of an enemy after it's death.
Liches also sometimes have these, held in some hidden or well-guarded locations. Except for Kel'Thuzad, who carries his with him, possibly because it would be difficult to find a better guard for it than he himself. Or they could just give them all to Arthas, meaning that their enemies would have to win the whole war to kill any of his liches. But Arthas seems to have some strange compulsion to get all his servants killed. This later turns out to be an odd compulsion of human Arthas's pride, trying to train new champions to corrupt.
Arthas' sword, Frostmourne, is a soul jar plus. When Tirion Fordring shatters Frostmourne, it releases the souls of every being it's absorbed, including Arthas' father. Its destruction also leaves Arthas vulnerable to a No-Holds-Barred Beatdown by the raid attacking him as Arthas' soul was bound to the blade from the moment he first picked it up.
Subverted by Makai Kingdom: Badass Freaking Overlord Zetta is forced to use a book for an impromptu soul jar to save both himself and it when everything else in his Netherworld, including his original body, is destroyed. This essentially leaves him a sentient tome whose lack of arms, legs and a Netherworld is a significant step-down from his previous situation - and to make matters worse, he has no way of returning things to normal on his own. He still has all the Mana he did when he had his body though.
Played to some degree in The Elder Scrolls, where you can capture monster souls inside "Soul Gems" by casting Soul Trap and then killing the monster; you can then use them to enchant items, recharge them, or you can sell them for an insanely high price.
In Morrowind, The Heart of Lorkhan acts as a Soul Jar for the Tribunal and Dagoth Ur. Unbinding it renders them all mortal, as the heart is what gave them their divinity in the first place.
In Daggerfall, the Underking's soul is bound to the Mantella, a soulgem used to control the giant golem Numidium. As long as it exists, so will the Underking. Subverted in that The Underking is looking for the Mantella to destroy it - he wants to die, and does not care about the giant golem everyone else seeks to awaken for their own purpose.
Oblivion also lets you do this to people, but it requires a special type of "black" soul gem and is considered a form of evil magic (though there's no consequences for doing it). A human soul has the same strength as a high-end monster's but you can get them long before you run into said monsters; essentially, hard to find, easy to fill. One of the Dark Brotherhood targets in Oblivion is a mage attempting to become an immortal lich. Part of the process involves putting his lifeforce into an hourglass which he has to keep on his person at all times until the transformation is complete, otherwise he dies. This gives the player an obvious method of killing him.
In Skyrim, the insane necromancer Malyn Varen successfully managed to pervert Azura's Star into housing his soul, in his quest to live forever. Cleansing the star of his soul is a part of Azura's Daedric quest.
In the Dawnguard DLC for Skyrim, it's revealed just what happens to the creature or individual trapped inside of a soul gem after it's been used up. They are sent to the Soul Cairn, a graveyard realm of Oblivion where they suffer in torment for the rest of eternity. Still comfortable using Black Soul Gems to power your weapons and armournow?
One can fight many liche lihc in Kingdom of Loathing but you can only find one phylactery for a Mid Boss version. You could "kill" it without the item, but destroying the phylactery results in an instant kill.
In the freeware platformer Hurrican, the Big Bad is reduced to a floating robot skull after the penultimate boss fight, which soon attaches itself to a giant killing machine for the real final battle. To win, you have to reveal his organic heart, kept behind a reinforced steel wall, and smash it.
In the very first Ultima I game, Mondain the Evil Wizard has done this with his Black Gem. When you finally fight him, you see him in the process of making it. You can continually "kill" him, but it won't count and he keeps getting back until you've done so after destroying the Gem. Similarly, in Ultima V, the Shadowlords who were born from the shards of that Gem cannot be permanently killed unless their individual shard is destroyed at the same time they're immersed in the Flame of the opposite Principle of Virtue.
In some games, you can capture a Poe's soul in an empty bottle.
In Twilight Princess, Ganondorf and Zant are each other's soul jars. After Ganondorf "houses [his] power" in Zant, you can't kill one without killing the other. Zant's neck snaps by itself as soon as Ganondorf dies.
In System Shock 2 you face Psi Reavers - huge flying jellyfish who are a perfect blend of flesh and psi energy and as such will keep resurrecting until you destroy their brain which is hidden somewhere nearby in a secluded corner.
In the finale of Deus Ex: Invisible WarJC Denton is backed up by a Universal Constructar that will continiusly reassemble his body when you kill him.
In Fall from Heaven the wizard Tebryn Arbandi created one out of Abashi the Black Dragon: the 3rd most powerful being in existance. One of those is a god.
Phantasy Star Online: Dark Falz can use the player characters as soul jars. While bound to a character, any damage dealt to Falz will be inflicted to the character instead (even if said character is under the status of "invincible"). The players can either wait for the binding to wear off before continuing their attack, or just let the bound character die to break the link and make Falz vulnerable to damage immediately.
BlazBlue uses this in the case of the Susano'o Unit. The unit is a mechanical suit of armor that requires whoever enters into it have their soul installed into it, not their body. Terumi was the original vessel within the unit, but after the Dark War he ejected from it, becoming a literal ghost. Later on, the time-looped storyline shows that a dying Jin was transferred into the unit by Rachel. Now that he understands everything, he pulls a Heel-Face Turn and becomes Hakumen. Technically this means that Terumi is the original Hakumen, and then afterward in all other loops, Jin is Hakumen, but then this implies that there were only 5 Heroes at the time. Another reason Terumi chose not to stay within the Susano'o unit was that he was trying to destroy Amaterasu, and remaining within it would bind him to the very Master Unit he was antagonizing. The soul of one of the other Six Heroes, Trinity, is contained in her Nox Nyctores.
Dragon Age has examples, such as the Life Gem with the trapped Arcane Warrior's soul and the Black Vials holding the souls of the six Revenants scattered across Ferelden. Also, as revealed in Dragon Age II, this is how Flemeth survives her (optional) death at the Warden's hands: early on, while the Warden is still recuperating in her shack, she rescues the Hawke family from Darkspawn and gives them an amulet to deliver to Sundermount. If the Warden kills her afterwards, she is reborn from the amulet a year later thanks to Hawke. If the Warden doesn't, she simply uses the amulet as a teleportation beacon to travel to Sundermount undetected.
The "shards" used to power the terracotta army in Jade Empire.
In a variation, Charles Dalimar in the Return to Ravenhearst casual game uses a Soul Jar consisting of other people's souls, plus his own disembodied heart. This has evidently allowed him to remain in the world for generations, long after he should have died of old age. Charles apparently learned this trick from his father Alister; in Fate's Carnival we learn that Alister can only be killed by destroying a specific book.
In Guild Wars, Kurzic Juggernauts are linked to Forever Trees and can be reborn from them if the trees are intact.
In Shivers, each Ixupi is bound to a jar closed with a talisman. When one is reassembled, it will seal it away.
Skeleton warlords Styx and Stones provide a unique twist on this old chestnut. It is said that "as long as one lives the other cannot truly die." Meaning that to be permanently defeated they must both be killed simultaneously.
Cave Story has an inversion with the Demon Crown - the Demon Crown contains part of Ballos's soul, but rather than having to destroy the Crown to defeat Ballos, you have to defeat Ballos to prevent the Crown from reforming.
One of the tasks in Tak and the Power of Juju is collecting Lok's Soul Balloon so he can be resurrected. He's all squeezed up in there; tough balloon.
In Fable, Jack of Blades essence is held in his mask. If you destroy the mask, you defeat Jack for good. If you wear it, you become Jack of Blades.
The Sims Medieval has the spell "Soul Theft," which allows you to steal a person's soul fragment.
In Duel Savior DestinyNanashi is the soul jar of the legendary hero Rubinas, who died a thousand years ago. Perhaps somewhat unusually for this trope Nanashi is actually Rubinas' soul itself while what is called Rubinas is more akin to her will or memories, though still certainly alive.
In the old 8-bit action-adventure game "The Valley", you could create one of these (of type 2) for yourself by finding the six stones of the Amulet Of Alarian. The drawback was that this was single-use only; if you got killed, you were resurrected but the Stones were scattered, so if you wanted to be immortal once more you had to find them again.
Zig-Zagged in The Darkness II: According to Johnny Powell, there is no known working phylactery for regular mortals to be found in the secret histories. Doesn't stop people from trying, and ONE phylactery made for an Eldtritch Abomination succeeded, but the Darkness is already immortal and the Siphon failed to seal it long-term. Foreshadowing appears when it turns out that the phylactery meant for the Angelus actually failed...
In Demons Souls, the player character carries a crystal that collects the souls of recently fallen nearby corpses (enemies that the player has killed). Played with, in that this is anything other than safe for the soul inside; it's just stored in it.
Xykon in The Order of the Stick, is a lich, and naturally has a phylactery; his Dragon Redcloak's holy symbol. The phylactery is protected by so many spells he doesn't "even remember what half of them do". Another notable thing: Xykon's soul isn't in the phylactery except when his undead body is destroyed as noted in the prequel book Start of Darkness; Redcloack tries to ransom the lich by threatening to break it, and Xykon scoffs it off by saying he can make a new one to house his soul in any case. (By the letter of the rules in D&D this is true. For a lich to be killed you must destroy both the phylactery and the body.)
Homestuck fans should hope that Aranea's account of Cronus' Potter-style encounter with Lord English is true in explaining that the Jujus are essentially LE's horcruxes. One of which is Lil' Cal, which explains a lot.
In Guttersnipe, Lil' Ragamuffin survives being shot in the head and tossed in an incinerator, claiming that urchins don't need brains or bodies 'cause they're all heart, then shrugs off a shot in the chest because she keeps her heart in a bowl in a shack on top of an unclimbable trash heap.
Phylacteries in Angel Of Death. Every lich keeps their soul in a Phylactery, which can be anything from a Rubick's Cube to a book to a piece of jewelry.
Kamimura does this to his former pupil Goku in the first chapter of Broken Saints, with the fragment of Goku resting in Kami's own mind. This is how he receives the message that starts him on his quest. Goku is in a coma until Kamimura's mind is cleansed in the Grand Finale.
In the Hitherby Dragons story "Unclean Legacy", Francescu magically transfers all his life into one of his fingers, and then cut it off to keep it safe. When his brother Tomas snaps the finger he realises that a finger contains several bones. In The Fable Of The Lamb Sebastien the Hero mentions that he can survive a shotgun blast because he keeps his heart in a box
In Beast Wars, a piece of Rampage's mutant, immortal spark is removed and kept first in a squeezy-box torture device, then in the freakish Transmetal 2 clone of Dinobot. It is the part which remains in Rampage, however, that is his life, and when that is destroyed, the personality and memories of the first Dinobot are given to/reawaken in the clone.
In The Penguins of Madagascar, the baboons use "backwoods magic" to steal King Julien's "groove" and seal it in a jar until he gives them an apology for throwing a skunk into their pen. Julien, of course, refuses, and a fight for the jar ensues. It falls and breaks at Skipper's feet, who has remained skeptical about the whole "groove in a jar" thing until he starts dancing uncontrolably.
Galaxy Rangers has a villainous example with the Psychocrystals. The Queen sucks the life from her victims through an alchemical machine, puts that Life Energy into little red crystals, and uses them to power her highest-end Mooks.
Main villain XANA is an informatic version of this: since he is an A.I., he requires a computer storing his data to survive, meaning he will disappear if the computer is shut down. He solves the problem in season 4 by infecting hundreds of supercomputer all over the world to store his data.