I encountered someone who complained that whenever atheists tell jokes it's always about religion, never about atheism or atheists. He eventually clarified that we never allow anything funny and offensive about ourselves. I have to concede the last point; I can't think of any jokes about atheism or atheists that I would find offensive.
Here's what I came up with:
Q: What did the atheist say after walking into a church?
A: Mind if I smoke?
Q: How many atheists does it take to change a lightbulb?
A: One, and it's not funny!
Q: Why did the atheist die at the bottom of the cliff?
A: He didn't believe in gravity, either.
I realize it's a short list, so I invite anyone to come along and suggest some more. Bonus points if I find it offensive to atheism.