I've never been to an atheist conference, but here are a few that took place in other states this year:
American Atheists Convention - Atlanta, GA
Freedom From Religion Foundation Convention - Seattle, WA
American Humanist Association - Phoenix, AZ
Texas Freethought Convention - San Antonio, TX
Secular Student Alliance - Columbus, OH
The Amazing Meeting (not specifically atheist, but a lot of atheists attend) - Las Vegas, NV
Some of these change cities each year. The Atheist Alliance Internation Convention is in Los Angeles this year and was in Long Beach, CA last year, but was held in Washington D.C. in 2007 and Kansas City in 2006.
They're not all in California. We have one coming up in Melbourne, Australia next March. Speakers include: Richard Dawkins, PZ Myers, Dan Barker, Peter Singer, Taslima Nasrin, Stuart Bechman and heaps more. It's going to be the largest gathering of non-theists in Australia's history.