If you're an out-of-towner and you're looking to buy, American Cyclery is good because they have pretty much anything you want in stock. Sherrif star campy hubs? Check. DA7600s? Check. NJS parts up the wazoo? Check. Cinelli track parts? Check. Instant gratification. Pricey as hell, though. Definitely a nice place to wander around and look at stuff.
Freewheel Hayes seems like a great bike shop, but I think a person who lives in SF is much better able to appreciate it. If you just walk in and look around, there's not really much to see, and there isn't a crazy amount of inventory. They can get anything you want in a few days though (as they did for me while I was there... hello yellow strong-g grips!).
Jitensha Studio in Berkeley is worth a visit. It is a shrine. More boutique than bike shop though.
As far as Montano Velo goes, learn from my mistakes. They close at 5:30.
In any case, a proper SF vacation should be structured around eating moreso than looking at bike stores.
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