These are places we frequent where we know we can get solid service, the food sourcing is responsible and we don't get any flack when we have to omit or change things on the menu for our dietary needs. This list is far from exhaustive and is in no particular order.
M & G Burgers
Salad/Food Bar at Good Earth
Sula and Farley Bar
C Casa--Innovative kitchen at Oxbow Public Market and Emeryville Public Market
The Left Bank
Mill Valley Beerworks
FarmShop (restaurant link here)