Well in Berkeley the ones I know of are Missing Link, and Mikes Bikes. Missing Link sells Treks, Mikes Specialized, and Cannondales (I think). Both are descent shops. Missing Link sponcored CalCycling for a while. This year they switched to Mikes.
Personally I like Cannondale CAAD8 frames. It's a solid pro level frame.

Personally I used a bike shop in San Leandro. It was near to where I lived. Forgot it's name thought.