I might have missed it somehow, but how has no one mentioned
Chez Panisse ? While I think it has gone a little bit downhill in recent years, it's still an incredible dining experience.
As for my other random culinary favorites in the Bay, I really, really like
Legendary Palace in Oakland Chinatown, St Francis Creamery in the Mission (couldn't find a link, but it's quite the popular spot),
Kirala in Berkeley for Japanese food, and the gem of them all,
Cinque Terre Restaurant , which is unquestionably the best value for Italian food in all of North Beach, and comes close to rivaling some of my fave spots in Boston's North End.