Montano Velo in Oakland. Very small on-hand selection but the owner is a great guy and will get you what works for your needs. I've been going there for several years. Road, track, cross, touring...

Cycle Sports in Oakland... I tend to go there when Montano is closed. I've bought everything from a complete bike (CAAD9 MUSA back in the day) to small parts. They've always been incredibly friendly no matter a tube or a wheelset purchase.

King Kog in Oakland; buddy works there from time to time as a mechanic. Nice mix of new/used. Road, track, cross bikes.

Mike's Bikes in Berkeley. I never really went there for advice about anything, bought a Raleigh RX2.0 cross bike (sale...) a few months ago and some S Works road shoes years earlier. Always treated me well. Probably your best bet for a large selection of built bikes to tool around on. They've never pushed any kind of sales or service plans at me but then again I tend to just say "no" and move on.