Azazel promises to resurrect John so Mary can have a normal life with him if she gives Azazel permission to enter her house in ten years. Though Dean tries to intervene with the Colt, Mary makes the deal and John is resurrected while Azazel flees Samuel's body before he can wake up with no memories of being dead.
Of course, that was after John's death, which occurred in the season two opener, In My Time of Dying when John sacrificed himself to save Dean. Needless to say, there's a lot Sam and Dean probably never got to say to their dad before he died.
