(These comments are prefaced by the fact that it's been a year since I've lived in the Bay Area, so YMMV)
If you have a car, you may want to check out Gator Games in San Mateo; they have a fairly friendly staff and a very good selection. Scenario Games in Fremont is pretty good, although it leans more towards boards games and model railroading, and a discussion on these boards a few months ago mentioned that they may be forced to move out of their location on Fremont Blvd. The Berkley game shop is very disappointing, IMO, but if your only mode of transport is BART, it's worth stopping by if you're going there to hit some bookshops, too (like Another Change of Hobbit, a decent science fiction shop). Another excellent SF/fantasy bookshop is Dark Carnival, but as far as I recall, it's not within walking distance of a BART stop, and it has little in the way of gaming, although it may be the best SF shop I've been to.
Enjoy!