La Trappe (specializes in Belgian beers, their beer menu is inch thick)
City Beer Store
Definitely schedule a tour of Anchor Brewery if you can. And if you are here on Sunday, get out to Santa Rosa to Russian River Brewpub for an all day happy hour - the only place you'll find 12oz of Consecration for $3.25.
Don't forget Anchor Brewing. I don't know if this is a regular thing, but I went there and enjoyed a free tour complete with a free beer tasting session which included 6 different beers, each in an 8-ounce glass.
If you get to the North Bay, a great day would start with Moylan's for lunch: Untitled Document
then stop by at Lagunitas tour every weekday at 3:00 PM (they don't advertise, but show up and get free beer) Lagunitas Brewing Company
and end the tour at Russian River for dinner: Russian River Brewing Company
This tour will give you some of the best beer in Northern Ca.
Stop by bear republic for the beer and come out to the winery I work at David Coffaro and I will taste you through wine if there on the weekend. I make wine there and would be more than happy to give you a taste of the good stuff.
Since you are going to napa, hit up Napa Aleworks(?) or something like that. It is a brewery on that side of the mountain, but of course Napa is a great place for Auto parts, Sonoma county is a great place for wine
+1 million on going to Russian River brewing. I was just there for the 1st time and Pliney the Elder is absolutely the best beer I have ever had. I highly suggest making the trip up there and the Pizza was awesome to boot, you could also run over to Third Street aleworks while your in Santa Rosa.
Edit: of course you can probably get Pliney the Elder at one of the pubs in San Fran.