There isn't much in the way of explicitly atheist cinema* -- that is, movies that contain the explicit or implicit message that religion is nothing but superstition, and where this point itself is a central part of the story. The only popular films that jump to mind here are The Invention of Lying, and to a lesser extent The Man from Earth (overall a phenomenal movie, but far less well known). Sure, there are lots of popular movies that make fun of organized religion, or what some people might call religious "fanaticism" (e.g., Dogma, Saved, The Life of Brian, Jesus Camp). But pretty much all of these come away with the message that it's fine to be "spiritual" or whatever, so long as you don't hurt other people, and don't get too crazy about what you believe. As much as some "conservative" pundits love to accuse Hollywood "liberals" of being godless, there sure aren't many movies where godlessness is really taken seriously.
And that's unfortunate, in my view, as movies are probably the most prevalent and influential art form for the general public, and because many people will form their views on abstract concepts based on the percepts that movies provide (related to the issue of generalizing from fictional evidence). One need only glance over the examples on the tvtropes page "Hollywood Atheist" to see that movies and television aren't exactly putting the best foot forward for our kind.
But perhaps there's a bit more hope in the way of non-theist cinema, as opposed to overt atheist cinema. Of course, any story without gods is a non-theist story, and there are plenty of movies that don't touch on gods or religion at all. But what I'm talking about are movies where one would normally expect to find religion, but where no religion is to be found -- in other words, movies that seem to be depicting the alternate world where humanity never fell prey to this particular superstition, and where the concepts of god and religion simply don't exist.
The movie that inspired this particular thought was 50/50, the recent comedy-drama where Joseph Gordon-Levitt plays a man dealing with potentially fatal cancer. It's a great movie, but what struck me afterwards is how completely absent any mention of god, religion, the afterlife, etc. was in a movie about a man, along with his friends and family, potentially facing his own death. There are lots of characters, lots of conflicts, lots of different perspectives on what he's going through, but nothing at all from anyone amounting to a "spiritual" response to the situation (at least that I recall).
And it got me thinking, what other sorts of issues are there where we would normally expect religion to pop up, such that a story without it would be decidedly non-theist, as opposed to incidentally non-theist? And are there other major movies that you think tell such a story? I ask both because I'm always eager to hear about new movies I might enjoy (or old movies I might appreciate more), but also because I think this sort of non-theist cinema might be a good bridge to people who would instinctively rebel against anything openly atheist. In other words, show people that a "godless" world really isn't all that crazy, that people get by just fine and find ways to face conflicts, etc. Anyway, just thought I'd poll the membership and see what people thought about this idea. Looking forward to seeing the responses!
*I'm well aware that there's quite a bit of atheist and non-theist art in other mediums -- sf literature most prominently. But I'm focusing on movies (and perhaps to a lesser extent, television) because those are the main forms of "public art" in our culture, and the mediums most likely to influence how the public at large views these concepts.