Amoeba is the biggest game in SF if you want quality - the prices (for classical) are pretty good. Their $1 classical record bins often have some very decent stuff. Ditto with the Berkeley Amoeba. Stores like Streetlight and Rasputins are worth a drop in even though their stock is small, mostly because they're less knowledgable with classical and occasionally underprice a rare album by a considerable margin.
Saturn Records in Oakland/Berkeley has a good selection of moderately high end stuff - if you're willing to splurge $10 you can find some worthy purchases there. They're fairly sharp - with an active internet business, so it's rare to find an undervalued item. In fact, the owner sometimes comes across the bay and cruises the SF record stores for underpriced lp's.
The thrift stores in SF are a waste of time if you have a life AND you're looking for "collectible" records. There are some decent $1 records once in a while, but the good ones are gone long before you get there. Most are before the public has a chance to see them, and the rest go to a few Ebay hustlers who check every store early every day.
If you want the best shot at glory, Estate Sales - advertised on Thursdays in the S.F. Chronicle - are the way to go, but you have to be prepared to go EARLY on a Friday AM and wait with the other sharks. If it's a good one (and the word does get out ahead of time) record buyers will be there at 4 or 5am for 9am start.