Viridiana: A woman who wants to become a nun, gives up and does something useful with her life, after almost being raped twice. There's a mock Last Summer with homeless people that's really funny. The movie got Bunuel kicked out of Spain, because the Catholics were mad and Franco supported the church. I haven't watched Bunuel's other films (sans Belle Du Jour). Exterminating Angel sounds like it could be an "atheist" movie. He's famous for the quote, "Thank god I am an atheist."
The Wicker Man: Howie's a jerk Christian. He travels to an island in search of a little girl. He pisses on the local pagan customs. They burn him in a wicker man, while doing a Scottish jig.
Thirst- A priest becomes a vampire. There's lots of sex.
Quest for Fire= It's about cave people. Their lives sucked. They go after fire. There is cannibalism.
Crimes and Misdemeanors= A dentist kills his mistress, gets away with it. He contemplates turning himself in. Woody Allen loses Mia Farrow to a jerky Alan Alda. Woody also stuck to his principles, and he got screwed. The universe is random is basically the point of the movie, and Woody Allen thinks that sucks.
Inherit the Wind of course. We had to read and watch that one in high school.
Aguirre seems like it could be classified as an atheist movie. The conquistadors float off in to the jungle, and die.
There's a movie called Don't Torture a Duckling. It's about a priest that kills little boys so that they won't be corrupted. Not a very good movie.
Elmer Gantry is a good "atheist" book, don't know about the movie though.
I'd say Dawn of the Dead, Land of the Dead, Day of the Dead, and Night of the Living Dead were all kind of godless.
I recently saw Casper again, and I realized that it belongs on this list.
There's death and ghosts and an "other side", but nothing deity-ish. I think that this movie may have actually had an influence that was key to the fact that I now call myself an atheist. It deals quite specifically with ideas of some afterlife, and it was contemplating that topic that I eventually recognized my atheism.
Sure, sure, Dr. Harvey asks Amelia "Are you an angel?" and she sorta looks like maybe she nods, but she doesn't do a good job of it and it's ambiguous what the answer is; she just goes on to say what she says as if to say "It doesn't matter what's up with me, James, I'm dead."
It's not an egg-breakingly atheist movie, but it is spoon-bendingly so.