Hans Solo, Star Wars
Stargate (movie and tv) I am surprised no one has mentioned Stargate (the movie) and even more so the tv show Stargate SG-1. The TV show has a running theme of destroying various religions that were created only as a means of control and the later seasons deal with an invasion of missionaries from another galaxy. The spin-off shows are not as atheistic but SG-1 clearly is.
It was until Don Davis died and Richard Dean Anderson quit the show. When they brought on Beau Bridges and Ben Browder to replace these two, the show started having hints of Christianity. I was very disappointed that the fundamentalist nature and tendency of the country to be intolerant towards anything perceived as non christian or other than christian managed to leak into my favorite show.
At least partially: The Contender.
I especially liked Joan Allen's answer on her being an atheist in her confirmation hearing:
"And, Mr. Chairman, I stand for the separation of Church and State, and the reason that I stand for that is the same reason that I believe our forefathers did. It is not there to protect religion from the grasp of government but to protect our government from the grasp of religious fanaticism. Now, I may be an atheist, but that does not mean I do not go to church. I do go to church. The church I go to is the one that emancipated the slaves and gave women the right to vote. It gave us every freedom that we hold dear. My church is this very Chapel of Democracy that we sit in together, and I do not need God to tell me what are my moral absolutes. I need my heart, my brain, and this church."
The Ledge - coming in June 2011
To be clear the main character is Hypatia - and the action of the film is in Alexandria, Egypt. Rachel Weiss in the main role is spectacular!
I love that this film does not shy away form showing the Christians as an unruly mob of violent self-righteous thugs! ... so not much has changed since!
I HIGHLY reccommend this film!