In the SF Bay Area. Unfortunately there's really only Guitar Center and Rocker Guitars in the city itself that carry anything worthwhile. GC isn't all that bad, depending on whom you get to help you. But my experience is about 50-50 there. And I've been there quite a bit in the past. Which probably doesn't say much for their service.
Rocker Guitars on Howard St. is one of those stores where you're going to get scoped out immediately by whomever is behind the counter. If they can tell you're not serious about buying anything. Then don't bother asking for assistance. I think part of the problem is that they're also located in a slightly shady part of town. But they do have an impressive collection of Charvels and Gibsons there.
Up north of the city in San Rafael is "Bananas At Large". Which is one of those legendary mom&pop stores. Well worth the visit, just to check out the town of San Rafael also. Awesome staff and their prices arent that bad. If you do visit, ask for Rick.
South of San Francisco are 2 more stores worthwhile checking out. One in San Matteo called "B Street Music" which carries a decent collection of Ibanez and ESP. I tend to see quite a bit of instruments on consignment there. So if you're looking to buy used, or NOS. You might want to make the trek down there.
Finally, further south in Redwood City is Gelb Music. They're probably the highest-end music store in the Bay Area. They carry PRS, Tom Anderson, Mike Lull, and high end Gibsons and Fenders. There's some serious guitar porn being exhibited at that store. But they also have a used instrument store around the back that has some good deals.