Dan Gordon's (formerly Gordon Biersch) brewpub at 640 Emerson in Palo Alto:
dangordons.com
Palo Alto Brewing;
http://www.paloaltobrewing.com/ has a tap room at 233 University Ave, Palo Alto
Rose and Crown, British-style pub with a good selection of beer at 547 Emerson St, Palo Alto
The Dutch Goose in Menlo Park. Not necessarily the best beer selection or food, but it has been there since 1966 and is prominent in the history of Stanford University and the rise of Silicon Valley. Worth a visit just because of the historical significance:
dutchgoose.net
Tied House brewpub in Mountain View, and AHA members get a discount:
https://www.tiedhouse.com/Freewheel Brewing Company brewpub in Redwood City:
http://freewheelbrewing.com/Alpha Acid brewing in Belmont has a tasting room:
alphaacidbrewing.com
Then there is my house in Palo Alto, with a good selection of beer but an unpredictable menu! Send me a private message if you want more information on the area. San Jose has quite a few brewpubs, too.