According to an article in today's Washington Post travel section the best cities for biking in are (in no particular order):

New York City, NY
Denver, CO
Portland, OR
Seattle, WA
San Francisco, CA
Davis, CA
Boulder, CO
Tucson, AZ
Madison, WI
Chicago, IL
Austin, TX
Philadelphia, PA

I think this is based mostly on the amount and quality of the bike trails, but it's not very clear from the article what criteria were used. Anyway, I thought that some might find this interesting.