The Alembic up in the Haight Ashbury:
http://www.alembicbar.com where I unhesitatingly recommend the Jerked Duck Hearts and the Bone Marrow.
Absinthe Brasserie:
http://www.absinthe.com/ where everything is good, ESPECIALLY the cocktails.
And Chez Panisse:
http://www.chezpanisse.com/reservations/ in Berkeley. Chez Panisse essentially invented the idea of five-star local cuisine back in the 70's and the food is seriously, seriously good. There wouldn't be a French Laundry if there hadn't been Chez Panisse.