John was a US Marine, presumably until he met his wife, Mary, and settled down in Lawrence, Kansas with her. In Lawrence, he co-owned a garage with his friend Mike. After Mary's death, he visited a psychic named Missouri. She showed him what was out there in the world and he realised that what he'd seen the night of Mary's death could be explained, even if no-one wanted to believe him. He brought the boys up by himself, all the while searching for answers about what exactly it was that killed his wife. He learnt as much as he could about the supernatural and trained himself and his sons to fight evil in whatever form it took.
When Sam left home to go to college, John continued to work with Dean, until he went missing while on the trail of a White Woman in Jericho, California, he left Dean a voice-mail message warning him to be careful. Dean and Sam searched for John for months with no sign of him. Little did they know that when they went home, he was there, hiding out in Missouri's house. Later he phoned the boys from a payphone in Sacramento, California. He was not heard from until Sam and Dean believed they had found the demon they were all looking for in Chicago. It was a trap, however, and all three were nearly killed by a Deva. John parted ways from the boys again in order to protect them.
When they finally got back together, it was with a greater chance of defeating the Demon. An old friend of John's left him a mystical gun that would be able to destroy the Demon. The three of them faced the Demon, but tragedy struck when their car was smashed into by a truck whose driver was being possessed by the Demon. John and Sam survived with little wrong with them, but Dean wound up in a coma. When John realised his eldest son was going to die, he made a deal with the Demon - offering the gun and his own life in exchange for Dean's. Minutes later, Sam found John laying dead on the floor.
The boys cremated John's body in a pyre, taking his US Marine dog-tags to Mary's headstone so that the two of them could share something.
John's headstone could be seen in the episode What Is and What Should Never Be. Although this was an alternate universe, it is fairly certain that his year of birth and middle initial as shown on the headstone would be the same in the regular universe.

Quotes about John

Dean : I love the guy, but I swear he writes like freakin' Yoda.
-- Asylum
Sam : When I told dad when I was scared of the thing in my closet he gave me a .45.
-- Pilot
Meg : ... You see, he has one weakness.
Dean : What’s that?
Meg : You. He lets his guard down around his boys. Lets his emotions cloud his judgment.
-- Shadow

Quotes by John

"It knows I’m close. It knows I’m gonna kill it. Not just exorcise it or send it back to hell. Actually kill it."
-- Shadow
Sam : Dad, you don’t have to worry about us.
John : Of course I do. I’m your father.
-- Shadow
"I want to stop losing people we love. I want you to go to school. I want, I want Dean to have a home. I want Mary alive. I just... I just want this to be over."
-- Salvation
"So somewhere along the line I stopped being your father. And I became your drill sergeant."
-- Dead Man's Blood

John Gallery