What a great thread... Having worked in shops for years, it's now gotten to the point that I can't pass a bike shop without going in. I was super lucky and got to write a magazine article about the great shops in my area, and it was so much fun.As far as a favorite goes, I can't narrow it down to just one...
American Cyclery, San Francisco
Stone's Cyclery, Alameda
Left Coast Cyclery, Berkeley (woman-owned!)
Cyclepath, San Mateo
Cupertino Bike Shop, Cupertino

okay, i think that's all of them...