I'm still on my first cup of coffee so this won't be that complete but....
Full disclaimer: I live in Oakland.
21st Amendment brewery
Toronado Draught Beer List
Anchor Steam brewery. People rave about the hour long tour, which I've yet to do.
The Thirsty Bear brewery and tapas restaurant. It's in downtown, near the SFMOMA and Yerba Buena Gardens, and on Sunday nights has free flamenco shows.
Beach Chalet brewery. Never been but it's at the end of Golden Gate park and looks out over the pacific.
Magnolia Brewery, restaurant pub, on Haight street. Heart of the Haight /Asbury area.
I like the fish and chips at the Irish Bank. In between downtown and the edge of China Town. Hard to find.
Cross the bridge to the East Bay
Barclay's pub (30 taps)
Barclays College Avenue - Today's Beer List
The Trappist, downtown oakland, hundreds of bottles
The Trappist, Belgian & Specialty Beer
Trumer Pils in Berkeley
Jupiter's, beer garden with great wood fired pizzas serving Triple Rock brews
If you are driving around the bay area, as in an hour or two of driving:
Russian River brewery in Santa Rosa, home of Pliny, which many would consider worth the hour and a half drive, though you can get it at local pubs too.
Half Moon Bay brewery in, you guessed it, Half Moon Bay. Try the poke tuna and a pint, outside looking at the bay, then go to KetchJoanne's for dinner, which is the locals' seafood.
For an overnight in HMB, call on a thursday, or reserve ahead to get a "private room" at the Montara Lighthouse hostel. $65, basic nice room, in a lighthouse, on the cliff. The "dorm rooms" are what they sound like.
Point Montara Lighthouse Hostel - Welcome to the Point Montara Lighthouse Hostel
Bear Republic Brewery in Healdsburg
Lagunitas in Petaluma
non beer related stuff in SF
House of Nan King, chinese food, get the sesame chicken
...uhm.... guess I can't think of any more non-beer related items right now.
The new California Academy of sciences is getting great reviews. Go early in the day so you can get tickets to the planetarium, which sells out everyday by about 11:30am. I still haven't made it in. The Tea Garden near by in GG Park is also a nice place.
Bring walking shoes. And you'll find lots of cool stuff, around any of those places I just listed.