I am assuming no kids, correct?
San Francisco City highlights-De Young Museum, Steinhart Aquarium and Japanese Tea Garden-All in same area of Golden Gate Park
Alacatraz, Bay Boat Tour and Fisherman's Wharf
Marin County and North Coast-Muir Woods or continue heading north on 101 to Redwood National Forest.
Sonoma County Wineries and Napa County Wineries-I would suggest doing these on separate days, one winery in morning, lunch, second and possibly third in the afternoon.
Napa County suggestions other than one of your personal favorites would include Castelo di Amoroso(V. Satui),
http://www.castellodiamorosa.com/. Auberge du Soleil and Beringer.
Also, try to plan a day or two in Santa Cruz and Carmel/Monterey area.