One answer : Toronado.
It is a cool bar with a simply awesome range of beers.
I'll edit this post soon with more recommendations when I unpack my notes from last year.
Oh, one question, how far are you willing to travel? If you've got a car, do you mind taking weekend day trips out to say Santa Rosa? Would even driving down to LA or San Diego be an option? Let me know....
edit:
Ok, heres the places I visited. I only had 3 nights there and my fiancee was injured, so we didn't get a chance to visit many:
21st Amendment (Brewpub)
http://www.21st-amendment.com/
I really enjoyed this place. Really tasty double IPA, some good canned beers (suprising!) and the food wasn't bad either. Laid back, though I have a feeling it could get pretty college-like on a game day.
Jacks Cannery Bar (Bar)
http://jacksbarsf.com/index.html
Ok, this place was crap. Not only were the beers sold in plastic cups, but the range of "110 beers" was mostly macro lagers. We ordered food, waited half an hour (watching the chef chat with the barmaid) then cancelled our order and left. Worst service I recieved in the US during 4 weeks in 5 states.
Thirsty Bear (Brewpub)
http://www.thirstybear.com/
I was a bit dissapointed with this place. Overpriced food and some pretty boring (and in some cases shoddy) beers. If you're in the area i'd still drop in though as they do make a good Stout.
Toronado (Bar)
http://www.toronado.com/
This place was simply awesome. Ok, it's pretty dodgy looking, but the beer more than makes up for it. One of the best beer lists in the US, with some awesome micros and rare belgians too. I wouldn't be suprised if this becomes your "local" over there even if it's nowhere near where you're staying
Less than an hour north of San Francisco:
Bear Republic Brewery (Brewpub)
http://www.bearrepublic.com/
Friendly bar staff, brewers willing to chat and damn good beer. We had a lunch here too and it was pretty good. Recommended.
Bottle Barn (Bottle Shop)
http://bottlebarn.com
Pretty good range at this Santa Rosa bottle shop. Well kept beers, and some raritys from places like Hair of the Dog and other cool micros.
Lagunitas (Brewery)
http://www.lagunitas.com/
You'll need to call ahead to book a tour, but this is a cool brewery. Very laid back staff. We had a private tour of about an hour just chatting about beer & brewing. Oh, good beer too
Russian River (Brewpub)
http://www.russianriverbrewing.com
I don't really need to say much. It's Russian River. Definately in my top 5 personal US breweries. Amazing range of beers from hoppy double IPAs through to barrel aged flanders reds and beers brewed entirely with brettanomyces! Also worth checking out 3rd Street Aleworks, which is a few doors down. I didn't make it as it was too crowded the night i visited, but it's supposed to be an awesome beer bar.
Some other recommended places that I haven't been to:
Amnesia (San Francisco) - Bar with a good reputation, short walk from Toronado
Anchor (San Francisco) - Well, it's Anchor! They don't do tour on weekends though
Book in advance.
City Beer (San Francisco) - Supposed to be a really good bottle shop
Marin Brewing (North of SF) - Good reputation, I tasted some of the beers they produced in bottles and they were good)
Plumpjack (San Francisco) - Another recommended bottle shop
Speakeasy (San Francisco) - Another cool brewery, once againt tried their beers in bottles. They aparently do tours
Also, any Whole Foods Market is usually a good place to pick up beer. They're a specialist chain grocery store.
You should be able to google all the location for those ones