While prayer is used by those of religious faith, it is also used as a means of communication between humans, angels, and God. Nephilim can also receive prayer. Long before they knew of the existence of angel, Sam prayed everyday.
Dean prays for Castiel's help when he is trying to stop Sam from meeting with Lilith.
Looking to give himself to Michael as a vessel, Dean finds a preacher on the street and asks him to pray to the angels and to them them here is there. Castiel hears this prayer and arrives, beating Dean in anger before taking him back to Bobby's.
Castiel appears in response to Sam's prayer, when they want to try and get him to return all the souls to purgatory.
Dean prayers for any angel to help him, and many of the recent fallen angels answer his call, including Gadreel pretending to be Ezekiel.