In Napa, just walk the streets find any place that looks good to eat. Chances are it's amazing. Sonoma has some good lunch/brunch places. Sterling Winery is a must. I also went to V Sattui and it wasn't bad. If you rented a car, on the way between Napa and San Fran, take a detour and go to Stenson Beach and the Muir Woods. Definitely worth going there.
In San Francisco, like i said before in the thread, don't go to Alkatraz, but definitely take a boat tour around it. Unless it's a night tour, then do it. Golden Gate Park was pretty awesome. Chinatown and downtown in general was fun.