(1350 Coleman Ave., Santa Clara) by the San Jose Airport. EXCELLENT selection of games - one of the best I've seen in all my years of scouring Game stores.
Since moving to their new location they've done a great job of stocking a bunch of titles. I've seen a lot of game stores in the Bay Area come and go going back to the early 80s, but can't think of any that ever topped Game Kastle in terms of number of titles and large stock.
Having said that, its a stock of fairly new titles - if its in print or recently in print they've likely got it. Including some current releases not often carried elsewhere - got Viktory II there, something I couldn't find at most online shops. But its not a place to go for anything remotely out of print.
Legends - In Oakridge Mall in San Jose. Decent selection of games.
Also one in Valco Mall. Good selection for a mall store, but nothing worth making an out of town trip for, although they do also have a decent selection of collectibles (action figures, pop culture statues).
Others in the area that may or may not be still around:
D&J Hobby and Crafts
Campbell, 96 San Tomas Aquino Road - Campbell. Had a great selection of games at one time. I haven't been there in years though.
Selection has definitely gone downhill over the years. Can't believe the store I got my SFB fix from, that I picked up oddball gems like S.F.3.D. from, is now reduced to this. Still a fair selection of mostly newer stuff, but its no longer a place to find older gems and doesn't quite stay current enough to rely on for new releases near their release date. I get the impression this store, under economic pressures, has fixated on their primary income source of RC vehicles.
Gamescape - Palo Alto. I think this one has since closed up but there still may be the store in San Rafael (Marin?) with the same name.
Gone but not forgotten. One of the last stores to stock used games, and they had a great selection of new games. Game Kastle is a better mix for the latter, but Gamescape Palo Alto had a certain charm that will be missed. Probably my last "you still have this in stock?" moment at a game store was at Gamescape Palo Alto.
Gamescape San Francisco is still in business, but each time I make it up to the city it seems their variety diminishes. Maybe I'm just getting old and am not as easily impressed as I used to be, but I can't name a time in the past 5 years I've seen them have something on the shelf I wanted.
San Mateo, 4212 Olympic Ave - Good selection - small store but lots crammed in there.
Crammed is right. The place has less than half the floor space of Game Kastle, but a comparable selection. And they aren't hell bent on clearing out unsold stock, which means some nice older game finds can still be had there (picked up the final deluxe edition of Car Wars there two years back, new in shrink for MSRP). If you're looking for a place to play, this place is way too cramped and I'd give the nod to Game Kastle. But in terms of selection - specifically "can't just find these on any of a dozen websites or other game stores" titles - I have to give the nod to Gator Games. This is definitely a store to hit if you are ever in the area and like to browse, and possibly the only remaining game store in the area I can go to and not immediately get that bored "got it, got it, seen it already" feeling.
For those in the Berserkly area, Games of Berkeley is a great shop and the only other Bay Area store (haven't hit Endgame yet, Oakland is too far out of my way) to match Kastle or Gator in terms of selection. Just up the street from there is Eudemonia, which has a lesser (but still fairly good) selection of games but IMO is a better place to play due to the table layouts.