Guitar Showcase in San Jose is a really nice shop. I haven`t been there in a few years but it was loaded with guitars , amps and pedals . Can`t imagine it changed much . There`s also a consignment shop right next door
Starving Musician has shops in Santa Cruz , Santa Clara and Berkley. Haven`t been to any of those places in ages but they were pretty cool shops for used gear
Its in San Rafael, in Marin County, you have to cross the Richmond Bridge, its about a half hour from Oakland. The usually have a bunch of over priced used amps and guitars from Satriani and Neil Schon. Usually they have a good amp selection, decent guitar selection, and a TON of pedals. They say they will beat any price.
Guitar Showcase in San Jose. Maybe the best selection of Fender and Gibson in the south bay. Gelb Music in Redwood City is also very nice. Small shop, but lots of high end stuff. Good luck!
The OP might be long gone by now but I went to Vision Guitar this morning , the first time I`ve been to the current location. Man for a small store it`s freaking awesome. Just about every part and accessories under the sun. Cool selection of Suhr and Mcnaught guitars and Friedman , Suhr , PRS and Milkman amps. I could have spent hours in there just going thru all there accessories