It seems that it was coined by Hamilton Jacobi in a comment that (ironically?) was not allowed through moderation at The Intersection, but was reposted at Butterflies and Wheels. It was then picked up by Jerry Coyne, and it took off.
(Gnu atheist symbol stolen from Aratina Cage.)
Update: Five minutes after posting this, Jerry Coyne makes AC’s logo official. Strange synchronicity, or has Jerry subscribed to my posts? (Yes, I backdated this post from 11 Oct to 30 Sep. because I didn’t want it at the top of the blog. Let that be a lesson about messing with the time continuum.) [edit: Or perhaps the WordPress pingbacks deserve credit? Can you tell that I’m not a skilled member of the blogosphere?]