'The Invention of Lying' starring Ricky Gervais is pretty good.
Monty Python's 'Life of Brian'
'Letting Go of God' with Julia Sweeney isn't really a movie, just one of Julia's monologue stage shows, but worth watching. Julia is very relatable, funny, and her stories can still stir up some deeper emotions.
'The Sunset Limited' with Tommy Lee Jones and Samuel L. Jackson is a bit of a nebulous one. I think the characterizations of Jackson as a Christian and definitely Jones as an atheist are a bit stereotypical, to a point being a bit hamfisted about it. Jones's character doesn't really promote humanism, so his philosophy doesn't speak for all atheists by any means. And, it really doesn't try to give the viewer any answers, just makes them face some hard questions. But, they're both fantastic actors, and pour a lot of emotion into it.
