As for tv shows Star Trek, especially the original series had a lot of anti-religious messages. Apparently Gene Rodenberry was a big time atheist and specifically worked that into the show. It's also present early on in TNG, though after Rodenberry died the subsequent series became more about pushing the sort of vague liberal faith and spirituality. To the point where we got DS9 and the captain was literally a religious icon.
This year's remake of "Karate Kid." Actually, the original had no religious overtones either.
What really struck me in this year's version: For once we get a black family/protagonist that isn't draped in giant crosses or otherwise overtly (or at all) Xian. They aren't specifically stated at Atheist, but there's simply no religion at all.
There's a bit of superstition around the 'dragon well,' but by that point in the movie, it is shown as cultural and metaphorical, not so much as a literal belief.
Most of the obvious ones have been mentioned I think. There are a few I would add however.
V for Vendetta - focused more on anarchy, but the strong anti-authoritarian themes seem consistent with atheism.
Watchmen - another Allen Moore adaptation. This one is also quite anti-authoritarian. The character of Dr. Manhattan is brilliant (though I think that his character is somewhat more clearly portrayed in the graphic novel). The atheistic side of this story is made most clear through his character. "I don't think there is a god. And if there is, I'm nothing like him."
Fight Club - this was already mentioned, but I'm surprised it took so long and seemed to get such little attention...I recommend the rest of Palahniuk's books to anyone who enjoys the dark humor and satire in Fight Club. Survivor is very anti-religious and is hilarious. Invisible Monsters and Haunted are probably my favorites of his.
The Mist - another adaptation, the last one on my list. This one is also heavily focussed on its anti-authoritarian message, from the soldiers who were "only following orders" to the insane cult that develops as the story unfolds. The message here is to think for yourself, because when too many people let an authority figure think for them, authority transforms into tyranny.
Donnie Darko - I find it hard to believe no one has mentioned this, but I haven't seen it posted anywhere above. Donnie Darko is a dark, nihilistic drama with a little science fiction mixed in for good measure. The story itself is amazing, but even for those who don't appreciate the story itself, the philosophy presented here is extremely thought-provoking. (Watch the director's cut as the deleted scenes which were put back in make the story and philosophy surrounding it far more clear. Infact, even if you've seen the original cut and didn't like it, I recommend seeing the director's cut as you might change your mind once you understand it better.)
Franklin - This film seems to be relatively unknown, though it is still fairly recent (2008). It is by far the highest recommended film on my list. It appears very strange at first, but by the end it wraps itself back up nicely. I see it as four people each coming to lose their faith in the fantasies which once drove their lives and freeing themselves in order to deal with reality. I would recommend it to anyone (though it too is rather dark) especially any atheist.
I'm sure I've seen others, but they aren't coming to mind at the moment.
Fight Club and Donnie Darko are two of my favorite all-time movies. Fight Club is number one. American History X is number two. I am a big Edward Norton fan. Anyway, I don't know why I didn't list them in my movies.
Im actually after making a list of a few movies for my colleges atheist society. some are allready mentioned here but i think ill just put them all down. there are two catagories "serious" and "not so serious". there are also some we showed last year that arnt on the list (and some that are) but if i can get any more ill put them up.
1) the god who wasnt there
2) god the universe and everything else
3) letting go of god
4) Richard dawkins the root of all evil
5) Richard dawkins enemies of reason
6) Colission Christopher Citchens Vs Douglas Wilson
7) the story of god (3part documentary by the BCC
8) the four horsemen
9) jonathan millers Brief history of disbelief
10) the atheist tapes (not a movie a set of audio i think)
"not so serious"
1) Perfect parents
2) 2001 a space odessy & 2010 the year we made contact