The Arts & Faith website has a listing of the top 100 spiritually significant films. Go here for the list.
It should be noted that "The Passion of the Christ," Mel Gibson's film that made waves in the Christian community in early 2004 and was utilized in many church lesson plans, comes in at #35. I still haven't seen it.
Martin Scorsese's controversial "The Last Temptation of Christ" is #70.
"Eternal Sunshine of the Spotless Mind," a film that I expected to hate but ending up loving, is #98.