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In the episode "weekend at Bobbys" we find out that a spirit can be destroyed by burning it's earthly remains. After John Wincester died, Sam and Dean gave him a hunters funeral in which they burned his body meaning that his spirit should have been destroyed.
So how did he escape from hell in the episode "All hell breaks lose part 2"? Bearing in mind that his spirit should have already been destroyed.
The show confirms this a few times in later seasons:
Ash dies in "All Hell Breaks Loose, Part 1" and, because of the manner of his death, it's likely that his remains were destroyed at the same time (or that he received a Hunter's Funeral shortly after). However, we see him again in the season 5 episode "Dark Side of the Moon."
The episode involves Sam and Dean infiltrating Heaven; Ash grabs them and takes them back to his personal afterlife
Two Hunter characters are killed in "Abandon All Hope...", in season 5.
It's Ellen and Jo Harvelle.
The characters are killed by an exploding gas can, which they are sitting next to; assuming there were any remains left after that, the Brothers presumably gave them a Hunter's funeral.
Both of these characters are later seen and/or referenced:
Crowley has a line in the season 6 episode "Weekend at Bobby's" that also implies this:
Crowley: I loathe [Gavin, Crowley's son from when he was human]. You want to torture him, just let me pull up a chair and watch. Hell, burn his bones and send him down to me and we can have a family reunion.
Supernatural Season 6 Episode 4: "Weekend at Bobby's"
Late in season 7, a character dies, and is given a Hunter's funeral:
It's Bobby.
This character returns as a spirit starting just a few episodes later, tethered to one of his former possessions. The Brother banish him (by destroying the object in question) in the season 7 finale.
The character later reappears in the season 8 episode "Taxi Driver"; as part of the season-spanning macguffin plot, Sam has to go into Hell to retrieve his soul.
It seems as though a spirit whose bones are burnt just gets another visit from a reaper, and get ferried onto whatever afterlife they earned; this is the implication of a conversation with the rogue reaper Ajay in "Taxi Driver":
Ajay: I am the reaper who took [character from bullet point 4, above] to Hell.
Sam: [Character] in Hell? We burned his bones. Once we did that, it was over. End of story.
Ajay: Hmmm, not necessarily.
Dean: No, no, no, 'cause, see, [Character] was on the good side of things, and good guys go to the penthouse.
Ajay: Usually, mostly. Depends on who you know, what palms get greased. If you're on the King of Hell's no-fly list, no way you cruise the friendly skies.
Supernatural Season 8 Episode 19: "Taxi Driver"
It should be noted that there are other possible routes:
But neither of these really apply to John, so it's pretty clear what happened in his case.
Since a ghost/spirit is a soul that hasn't moved on, it can't be destroyed. As Jason Baker pointed out, there is almost always a physical link (hair, blood etc)-I seem to recall one episode where this wasn't the case but I'm spotty on details.
By burning the body in a Hunter's Funeral, the entire physical body is destroyed preventing an anchor for the soul to attach to. This forces the soul to move on.
In the case of John Winchester, he was taken to Hell because he made a deal to save Dean. When the Hellmouth opened, his soul was able to escape and go to Heaven.
