A couple people have already mentioned East Bay places, so I'll add a couple more:
- Trappist (around the block from previously mentioned Beer Revolution) has lots on tap at 2 different bars plus a huge bottle list (mostly Belgian as the name suggests, but plenty of other options too).
- Triple Rock in Berkeley (go upstairs to the roof patio if the weather's good).
- Jupiter, also in Berkeley (big patio, so its another great good-weather spot). Their house brews are made by Drake's brewery in San Leandro.
- Cafe Biere in Emeryville tiny place gets crowded fast but has good food too.
I could keep going, but since you did ask about S.F., not East Bay, that's probably too many already...