Solano Avenue Cyclery is a great store with friendly helpful staff.
Their service is efficient and they really know their stuff. The store not only sells bikes, but they perform regular maintenance and repairs on them.
They also carry a good selection of bike clothing and accessories.
They will help you find the bike made for you, and make sure that you are happy with it before you leave the store.
The brands they stock are Kona, Specialized, and Trek, and a few other brands I can't remember. They usually have a sale running every other month.