Nature of Souls
The human soul is not a rubber ball. It's vulnerable, impermanent, but stronger than you know. And more valuable than you can imagine.
– Death, 6.11 Appointment in Samarra
A soul is a person's essence, and what persists after death. In the natural order, souls are transported to the afterlife by Reapers, and with the supervision of Death. The reaper Tessa refuses to tell Dean, on more than one occasion, where she takes the souls. Known destinations of souls are Heaven, Hell and Purgatory.
In Supernatural, a soul separate from its body is visualized as a blinding white light. Death and Famine have transported souls in a doctor's bag and briefcase respectively. Angels can determine whether or not someone has a soul, or the taste of it, via a painful procedure in which the angel reaches inside a person to touch the soul.
Souls are a powerful energy source. Famine consumed them to strengthen himself, demons bargain for them, and even angels have traded in them.
When Castiel rescues Sam from Lucifer's Cage, his soul remains trapped in the cage until Death retrieves it for him. Without his soul, Sam feels no empathy, guilt or compassion. He is not evil, but rather lacks any moral compass, willing to resort to more questionable actions- such as allowing Dean to become a vampire to help them find an Alpha, albeit also knowing that there was a cure for vampirism- than he might consider when normal. While he continues to have physical needs for food and sex, he doesn't sleep, and has a high tolerance for pain.
Death reveals that souls are so powerful that even he can't break them. They can be damaged, but never broken. When ghosts are put to rest, their souls are not destroyed; they are simply ferried by a Reaper to their final destination, though it had been believed by many hunters to be "death" for them with oblivion waiting for them afterwards.
Demons are formed in Hell by the corruption of a human soul over time. Lucifer made Lilith into the first demon in order to mock God's creation of humanity. While in Hell, Dean eventually broke under Alastair's torture and started torturing souls himself, and so likely would have been transformed without Castiel's intervention. Angels are able to rescue souls from Hell, though this generally requires a massive incursion, but a human can rescue a soul as well if they can sneak into and out of Hell with said soul.
Other souls go to Heaven, although it is unclear what the criteria is for entrance. Raphael mentions devoutness as one possibility, which trumps all others, such as in Ken Lay's case. In Heaven, each soul has its own version of Heaven where he or she relives happy memories. According to Ash these Heavens are individual, except in the case of soulmates, who share the same Heaven. Sam and Dean appear to share the same Heaven. Most souls cannot leave their own allotted space, although Ash works out a way to move between them freely.
Purgatory is a spiritual realm where the souls of supernatural creatures such as Vampires and Shapeshifters go after they die. This place is not connected with Heaven or Hell, though Crowley said that it is adjacent to Hell. After resurrecting Samuel Campbell, Crowley has him tracking down high-ranking creatures, especially Alphas, so that he can question them about the location of Purgatory, which he wants for "development purposes." When Dean kills Leviathan boss Dick Roman, both he and Castiel get transported there without dying.
A vampire named Benny tells Dean there is a way a human can escape Purgatory, and he'll help Dean find it for Dean taking him through the portal. Dean escapes Purgatory with Benny's soul inside him, allowing him to resurrect the vampire. When Sam later escapes from Hell with Bobby Singer's soul, he carries it out of Purgatory in a similar way to what Dean did with Benny's soul.
When Dean is releasing Benny's soul from his body onto Benny's bones he speaks the words: Anima. Corpori. Fuerit corpus totem resurgent. Which translates as "Soul. Body. Whole body shall be raised."
Deals and Markers
Souls are first mentioned in relation to the deals made by Crossroads Demons, wherein a person agrees to give their soul to the demon upon death in exchange for some benefit when they are alive. Crowley was originally the head Crossroads Demon. The deals are traditionally sealed with a kiss, and have a set time limit at the end of which the subject of a deal, if still living, is killed.
John Winchester sold his soul to Azazel in exchange for Dean's life, and Dean sold his soul for Sam. Sam attempted to sell his own soul to bring back Dean, but the demons refused to make a deal as they wanted to keep Dean in hell.
Bobby sells his soul to Crowley to get information on Death's whereabouts in order to help stop the Apocalypse. Crowley is able to make the details of the contract he made with Bobby manifest as writing on his skin. The deal is undone when Bobby, with help from Sam and Dean, threatened to destroy Crowley by burning his bones.
The Power of Souls
Each soul a beautiful little nuclear reactor. Put 'em together, you have the sun.
– Eve, 6.19 Mommy Dearest
Crowley's interest in Purgatory, the resting place of the souls of supernatural beings, relates to the untapped power inside. Before her death Eve explains that her actions in rising from Purgatory, and mobilizing all the supernatural beings, are in reaction to Crowley capturing and torturing 'her children'. She speculates that Crowley is after the souls from Purgatory as together they would form a powerful weapon. 
Crowley's partner in the search for Purgatory is Castiel. Crowley convinces Cas that the souls there will give him the power to fight Raphael, as without some extra force he is no match for the archangel. A loan of 50,000 souls from Hell from Crowley allowed him to briefly overpower Raphael. Later, Atropos accuses Castiel of sinking the Titanic to create 50,000 more souls in order to "fund his war machine". She said that "he (Castiel) couldn't mint money, that it was wrong and dangerous and she wouldn't let him". 
Balthazar warns Castiel that if he takes in the souls of Purgatory, he may not be able to contain them and may explode "taking a substantial chunk of the planet" along with him.
When Crowley and Castiel finally determine how to access Purgatory and the souls there, Castiel cuts Crowley out of the deal, refusing him access to that power. Castiel opens the gate to Purgatory and absorbs all the souls, which allow him to destroy Raphael. He then declares himself a god. 
Balthazar bought the soul of a boy, Aaron Birch, in exchange for a part of the Staff of Moses. When asked why he bought it, Balthazar refers to souls as the only thing left of value; he is eventually forced to return it. Death hinted at the value of souls when he talked to Dean, saying that even he could not destroy a soul, or alter it. Death also said that a soul was "vulnerable, impermanent, but stronger than you know. And more valuable than you can imagine." .
Famine sought out the souls of others because of their power so he could strengthen himself by ingesting them.
The creature known as the Crocotta also consumes souls.
Angels can channel the power of souls. During a fight with Rachel, Castiel is severely wounded by an Angel Sword. The injury drains much of his power, making it impossible for him to retrieve Dean and Sam from the past. He tells Bobby that the human soul is pure energy, and if he touches Bobby's soul he might be able to draw on that energy to revitalise himself. Castiel says that done incorrectly, the procedure could cause Bobby to explode. Bobby agrees and endures great pain, and Castiel is able to bring back Sam and Dean through time from 1861. 
As part of a spell to travel through time, Henry Winchester uses his own soul as a power source, something that surprises Sam and Dean as they thought only angels could do this. According to Henry, he needs a week for his soul to recharge enough to safely travel in time again, though in desperation he tries to make the trip early despite the possible risks. 
Castiel: Somehow, when Sam was resurrected, it was without his soul.
Dean: So where is it?Castiel: Well, you pose an interesting philosophical question.
Castiel: My guess is still in the cage with Michael and Lucifer.
Dean: So is he even still Sam?
– Dean and Castiel discuss Sam, 6.07 Family Matters
After his return from Lucifer's Cage, Sam appears different, especially to Dean. He exhibits little compassion and Dean becomes increasingly suspicious that Sam may be possessed by Lucifer. Castiel refutes the idea, saying that if Lucifer were free they would know. It is eventually Veritas, the Goddess of Truth, who confirms Dean's worst fears that Sam is "not human" when he proves to be immune to her power. Sam admits that he knows something is deeply wrong. Dean calls on Castiel, who ascertains that Sam was resurrected without his soul.
Crowley claims that he pulled Sam out of Lucifer's Cage, but kept the soul "hostage" and that he will return Sam's soul if the Winchesters help him find Purgatory - a task he has had Samuel Campbell working on since his resurrection. Crowley later reveals to Dean, Sam and Castiel that he is incapable of raising Sam's soul from Lucifer's Cage, stating that raising Sam's body from the Cage was a very difficult task to perform.
Castiel later reveals that it was he who pulled Sam from Hell, but that he was not powerful enough to do it completely, thus leaving Sam's soul behind.
Once again, I went to harrow Hell, to free Sam from Lucifer's cage. It was nearly impossible, but I was so full of confidence, of mission. I see now that was arrogance...Hubris...Because, of course, I hadn't truly raised Sam -- not all of him.
– Castiel, 6.20 The Man Who Would Be King
For a while Sam continues to insist to Dean that he is still Sam - "same melon, same memories" - just without his soul, but Dean finally confronts Sam:
Dean: I mean, it's your gigantor body and maybe your brain, but it's not you. So just...stop pretending. Do us both a favor.
Sam eventually admits that "I'm not your brother. I'm not Sam". Then he confesses that he doesn't think having no soul is "better or worse, just different", but decides that he should get his soul back.
Leprechaun: The human soul gives off a certain perfume. Your soul is far away, but not completely out of reach.
He says that he could get Sam's soul out of Lucifer's Cage, but Sam banishes him.
Castiel and Crowley both predict that Sam's soul will have been tortured by Lucifer and Michael, and would be so severely damaged that it would harm Sam to have it returned, even drive him insane. Following this revelation, Sam decides he doesn't want his soul back, and summons Balthazar to see if there is a way to keep a soul out of its body. Balthazar informs him of a ritual that involves him defiling his body, that needs the blood of his father (that needn't come from the "father of your blood") to keep his soul out his body. This leads Sam to try and kill Bobby, only to be stopped at the last moment by Dean.
Sam is eventually reunited with his soul when Dean approaches Death for help. Death himself liberates it from Hell and personally delivers it back to Sam's body, despite his protests. Death installs it with the promise that a wall will be erected in Sam's mind which will prevent him from remembering his torment in Hell, but advises him to not "scratch away at it", lest the wall collapse and his memories come flooding back - though he suggests that this may happen over time regardless. Castiel says of the soul's condition once it is returned that it feels like it has been skinned alive.
As Castiel gets close to accessing Purgatory, he pleads with the Winchesters not to fight against him, but they refuse. Castiel touches Sam's forehead, which cracks the mental barrier that was planted there by Death, saying, "I'll fix him when this is all over". The breaking of the wall in Sam's mind causes him to have a breakdown; he is trapped inside his mind with the memories of what he did when he was soulless and what happened to him in hell. He manages to overcome this long enough to make his way to help Dean and Bobby in their efforts to stop Castiel. However, Sam begins hallucinating Lucifer and slowly goes insane until Castiel transfers the madness into his own mind, solving Sam's problems but driving Castiel insane instead. According to Castiel, Sam's hallucinations of Lucifer are an "aftertaste" of his time in Hell and simply projections of his own mind.
Dean makes a deal with a Crossroads demon and exchanges his soul for Sam's resurrection. The demon revives Sam and gives Dean a year. At the end of the time allotted in the deal, Dean's soul gets dragged to Hell and is constantly abused and tortured by the demon Alastair. After much painful torment, Dean agrees to torture other souls to stop his own torment. His soul is later retrieved by the angel Castiel and brought back to Earth.
In Season 5, Dean's stoicism and disinterest in the pleasures of life are discussed by Famine in terms of his soul.
Famine: Hunger doesn't just come from the body it also come from the soul.
Dean: Funny, it doesn't seem to be coming from mine.
Famine: Yes, I've noticed that.
Bobby, seeing no other way to locate Death, the last Horseman of the Apocalypse, sells his soul to Crowley to gain the Horseman's location. Crowley takes advantage of the deal to blackmail the Winchesters into not killing him, but also restores Bobby's legs out of apparent altruism with the deal. Crowley later reluctantly gives it back after Bobby threatens to have Sam and Dean burn his original human bones.
After his fight with Rachel, Castiel, severely wounded and drained of his power, finds it impossible to retrieve Dean and Sam from the past. He tells Bobby that if he touches his soul he might siphon off enough power to bring them back. Bobby agrees, but experiences extreme pain in the process.
After death, instead of going to his afterlife where he belongs, Bobby's soul stays behind on Earth as a ghost to help Sam and Dean. After his flask is burned, Bobby's soul is taken by rogue Reaper Ajay to Hell instead of Heaven on Crowley's orders as a result of what Bobby has done to him and his men. Bobby's soul spends the better part of a year in Hell before being rescued by Sam as part of the second trial to close the gates of Hell. Despite being little more than a ghost, Bobby's soul is able to physically interact with things without concentration and is carried back to Earth in Sam's arm as they escape from Purgatory. On Earth, Sam releases Bobby's soul towards Heaven, but Crowley intercepts it with the intention to take it back to Hell. Naomi intervenes and releases Bobby's soul, allowing it to rise to its true resting place in Heaven.
Souls in Religion and Lore
- Chassidic concepts of souls
- The soul in religion and philosophy from the Catholic Encylopedia
- Wikipedia entry on souls.
- The "human soul in the briefcase" device is a reference to the urban legend of the 1994 movie Pulp Fiction where the mysterious shining object in the briefcase (which is never seen or identified) is said to be the soul of Marsellus Wallace.
- ↑ 1.0 1.1 1.2 5.14 My Bloody Valentine
- ↑ 2.0 2.1 2.2 6.03 The Third Man
- ↑ 2.01 In My Time of Dying
- ↑ 6.20 The Man Who Would Be King
- ↑ 5.16 Dark Side of the Moon
- ↑ 2.01 In My Time of Dying
- ↑ 3.16 No Rest for the Wicked
- ↑ 4.09 I Know What You Did Last Summer
- ↑ 9.0 9.1 9.2 6.04 Weekend at Bobby's
- ↑ 6.19 Mommy Dearest
- ↑ 6.18 Frontierland
- ↑ 6.20 The Man Who Would Be King
- ↑ 6.19 Mommy Dearest
- ↑ 6.20 The Man Who Would Be King
- ↑ 6.17 My Heart Will Go On
- ↑ 6.21 Let It Bleed
- ↑ 17.0 17.1 6.22 The Man Who Knew Too Much
- ↑ 18.0 18.1 18.2 6.11 Appointment in Samarra
- ↑ 19.0 19.1 6.18 Frontierland
- ↑ 7.01 Meet The New Boss
- ↑ 8.12 As Time Goes By
- ↑ 22.0 22.1 6.06 You Can't Handle the Truth
- ↑ 6.07 Family Matters
- ↑ 24.0 24.1 6.10 Caged Heat
- ↑ 6.08 All Dogs Go to Heaven
- ↑ 6.12 Like a Virgin
- ↑ 5.20 The Devil You Know
- ↑ 7.10 Death's Door
- ↑ 7.18 Party On, Garth
- ↑ 8.19 Taxi Driver