If you are willing to go a little further afield, Livermore Cyclery (go to the one in Livermore, not the one in Dublin) has a phenomenal amount of stock on hand, knowledgeable staff, and a great owner (Steve Howard) who knows his stuff and is very friendly. I've known Steve for more than 40 years, and I can't enough good things about the store he has built up from scratch. I think it is the best shop in the Greater Bay Area, and not because Steve is a friend.

A little closer is Dublin Cyclery. Good people, good service. They will take good care of you.

Closer to you, I have had good experiences with Missing Link (Berkeley) and Sharp's (Lafayette). Stone's (Alameda) has an old-time feel and one of the long-time fixtures in the sport in owner Dennis Stone. The Pedaler in El Sobrante has done right be me over the years.

Any one of these shops will do you right. There are other shops that Forum members have praised, but these are the ones I can recommend based on personal experience.