In San Francisco I always go to "Healthy Spirits" at 15th and Castro.
Dave (the dude in charge) has an insane beer selection, but the best part about the place is that he has a "beer club". For about 45 bucks a month he sends out a newsletter that showcases all this hard to find beer, and descriptions of it. Sometimes he will do food pairings with it, but you go to the shop and pick up your beer from the club fee every month. More often than not, he includes beer that you can't really get in a store, just reserved for the club members. He is very knowledgable about the beer he sells, the whiskey he carries, as well as the wines. He'll talk your ear off about it, and its great because he makes his own hummus that you can buy there, and he has a sampler spread at the counter.
Talking about great beer, and chomping on homemade hummus.....rad.
I have had good luck finding rare beers at BevMo! in San Bruno. Was there yesterday and they had an amazing selection of holiday beers, including some holiday editions of belgian beers, such as Delirium.
I think Bottle Barn offers a great selection at fair prices. They are on Industrial in Santa Rosa for those curious.
Surprisingly the Costco in Santa Rosa has surprised me more than once with a good selection of cases. They carry on an irregular basis: Kona, Lagunitas, Sierra, North Coast as well as the "regular" premiums domestic, European and Mexican.