I just asked this question last week. Here is the list I was able to create:
Oakland -- Endgame; 921 Washington
Oakland -- Dr. Comics & Mr. Games; 4014 Piedmont Ave
San Leandro -- A World of Books, 137 Pelton Center Way
Castro Valley -- Epic Worlds; 3351 Castro Valley Blvd
Fremont -- Scenario Games 37120 Fremont Blvd., just south of Thornton; covers the whole gamut of games and hobbies; excellent)
Campbell -- D&J Hobbies; 96 San Tomas Aquino Rd
San Mateo -- Gator Games; 4212 Olympic Ave
San Francisco -- Gamescape (333 Divisadero, just off Fell St.; good for used stuff)
Redwood City -- Neutral Ground (more of a place to play games than a game store, but their D&D selection is pretty decent)
Palo Alto-- Gamescape on 465 S. California Ave
Mountain View -- Neutral Ground is located The San Antonio Shopping Center
560 Showers Dr, Suite 4
San Jose – Twice Read Books 81 E. San Fernando St
Livermore -- Fantasy Books & Games, 2247 1st St
Berkeley -- Games of Berkeley 2151 Shattuck Ave once you get off the BART.