the analog room is definately the place to go if you want to listen to some good old analog gear. Not even sure if they have any SS amps in there. Nice selection of speakers too: Avalon, Quad, Piega.
Also try Music Lovers in Berkeley. While not a tube shop, they do have a range of Wilson products (X2, WP7, Sophias) and Joeseph Audio gear. They have some CJ tube amps, not sure if they're using them though.
There's also San Francisco Stereo for Dynaudio, B&W, Rotel and Krell.
Audio Visions in San Francisco has Dali and JMRenauld, with bryston and sim audio gear.
There are many many more: Audio High in Mountain View, Paradise in San Jose.
Is there anything in particular you're looking to see?