Best Brewpub in the Bay Area?

San Francisco

As far as I can tell, there are only five establishments which are actual brewpubs in San Francisco. Gordon Biersch's beer is made in Palo Alto, and Anchor Steam and Speakeasy (regrettably) do not run pubs. Amazing, isn't it?

• 21st Amendment, South Beach (SOMA)
• Magnolia Pub, Upper Haight
• Beach Chalet, Ocean Beach
• Thirsty Bear Brewing Co., Yerba Buena (SOMA)
• San Francisco Brewing Co., North Beach

Berkeley/Oakland

I'm less well-acquainted with the East Bay, and may be missing one or two, but it seems like Berkeley and Oakland have no more brewpubs than the City:

• Triple Rock Brewery, Downtown Berkeley
• Pyramid Brewery, Gilman Street, North Berkeley
• Pacific Coast Brewing Company, Downtown Oakland
• Jupiter, Downtown Berkeley

Rest of Bay Area

Here I really don't know the options.  In fact, the only brewpub I'm familiar with is Gordon Biersch in Palo Alto.  I'm sure there must be others, but Yelp doesn't really distinguish between actual brewpubs and places which just serve many beers.  However, the excellent site Beer by BART does list a few:

• Marin Brewing Company, Larkspur
• Buffalo Bill's Brewery, Hayward
• E.J. Phair, Concord
• Steelhead Brewing Co., Burlingame
• Firehouse Grill and Brewery, Sunnyvale

Please Vote

Since I haven't been to all the brewpubs in the Bay Area, please vote from the above ... or add pubs I missed ... in the following categories:

1. Best Beer
2. Best Food
3. Best Service
4. Best Atmosphere
5. Worst Beer
6. Worst Food

When I have some votes in the comments, in a week or two I'll post my reviews of the SF and Berkeley/Oakland brewpubs and my opinion.