Endgame, in Oakland, has the best gaming space I'm aware of. About 10 big tables in a loft that circles the interior of the store. Pretty cool. Staff is cool, too.
GameKastle, in Santa Clara, is also a favorite of mine. They rent an entire office suite for gaming space. (However, the AC, if any, is pretty ineffectual, and it can get hot.) And the people there are really great folks.
In terms of store layout, I really like Games of Berkeley, but gaming space is cramped, and I don't really know the people.
I actively dislike GameScape, in San Francisco. No gaming space to speak of, the shop is cramped, and the staff is surly. God forbid you catch them in a game of Magic, and they have to interrupt it to answer questions or (gasp) ring up a purchase.