If you haven't played Dead Space, that is one game you should not pass up, especially if you enjoy survival horror. The game definitely has the undertones of a religion=cult motif. I actually played the game when I was still a theist and didn't see it but now that I am an atheist it's as plain as day. People like to compare the game's religion, unitology, to scientology and Visceral Games has repeatedly denied these accusations. However, I now more or less see all religions in the same light now that I'm an atheist and I wonder if Visceral does too. I see a lot of connections between Christianity and Unitology. Before playing the game you might actually want to view the animated comic which serves as its prequel. In this comic many of the main characters are athiests and are the only ones (to my knowledge) that are unaffected by the Marker - an alien artifact which makes the Unitologists suffer dementia and go on killing sprees. Seems to me that their religious fervor leaves them vulnerable to that sort of thing.
Definitely check it out. I'm a big fan of the Dead Space universe and if you'd ever like to discuss it with me I'd be happy to! :)
I wish I remembered which game it was (never played it myself), but there was an old Japanese game on the Super Nintendo where at the end, you kill God. If I remember correctly, Nintendo changed the ending for the American release.
Out of the games I've played, the one that comes the closest to atheism is Breath of Fire II (great game, by the way). In it, the world has started to embrace the church of St. Eva (a.k.a. Christianity). As the game progresses, you start to realize that the church is actually extremely evil and a lot of the supporters of the church won't see it because they can't face the possibility that their religioin is wrong. There's a particularly memorable scene where you have to fight against this paladin who is really a good guy that wants to help you, but he's not ready to turn against his religion.
Another game, although not nearly as blatantly anti-Christianity, is Final Fantasy VII. While the game doesn't really get into much religion, the villain is named JENOVAH, which is strikingly similar to the name of a particular God who I will not mention because I don't really want to be stoned by women dressed as men.
However, it is true that neither of these games actually had a character that was specifically atheistic.
Another game that may not immediately come to mind but actually was my inspiration at a young age to give up on false hopes is FFX. (Final Fantasy X)
I don't want to reveal story details but the game's religion, Yevon, was fairly...realistic and there are some dark things hidden within it. Again, you have to superimpose Yevon over Christianity or whatever religion you like to make it an "atheist's game," but that's probably all we'll get for a good while.
Dragon Age actually gives your character conversational options that seem atheistic and "The Maker" is a seriously absentee god of a deistic bent at best if we are to believe he exists in the context of the game at all. If you have Leliana and Morrigan in your party, they will eventually banter about religion with Morrigan taking an atheistic approach and Leliana expressing the theistic view. Alistair says a few blasphemous things that utterly surprised me out of nowhere. One was something about doubting the statues of Andraste (the savior figure in the religion) actually look like her, speculating that she could have bucked teeth or be ugly and they'd never know.
Vampire the Masquerade: Bloodlines also has religious themes and an atheistic sounding character in the form of Beckett. Beckett is basically a historian trying to work out how vampires came to exist. He scoffs at the religious terms and explanations others use and asserts that the only reason vampires accept such explanations is they are still clinging to the religions they believed as humans. Aside from the religious terms the vampires use to explain their origins the only other overtly religious material is a cult of diseased vampires that use *very* religious terms and phrases to explain their goals. I'm sure the game's designers did that to highlight the wrongness of what they were saying, but I found it darkly humorous. Sadly this game is rather badly bugged, but the most recent unoffical patch takes care of that issue handily.