Sorry, I didn't read through every post in this thread, but I've been thinking on this since Movie Bob posted his rant on movie stereotypes. A couple of his points talked about atheism in movies and they got me thinking about how we don't even notice it anymore because we see it as just normal instead of preachy.
The last movie I watched was Source Code. After reading Bob's post, I realized that this movie broke three of the stereotypes he complained about, two of those were religious in nature. Specifically, a character has a near death experience; there is no tunnel, no light, no vision telling him their is a plan, just empty nothingness before he awakes. This character is given another chance at life and he decides to live it out.
The difficulty in finding an "atheist movie" is that atheism is a belief there is no evidence of divine intervention. The atheist does not need to point out every time there is a lack of evidence of God because that is all times in his/her mind. To find atheist movies, look for scenes where a lack of God is conspicuous or auspicious. Disaster/apocalyptic movies, war movies, horror movies all do a decent job at leaving the viewer feeling abandon by any supreme being that might have helped.
Another thing to look for would be movies that give a definite alternative to God. Avatar comes quickly to mind. There, the planet takes the place of God. Beyond that, James Cameron throws the idea at us that we "already killed [our] Earth Mother." This is only one of many movies that suggest that the Christian God should be abandoned to the worship of nature, money, entertainment, government, etc.