I can't believe no one mentioned Pacific Heights and Cow Hollow in San Francisco. Pacific Heights is probably the most expensive area in SF, with incredible views and incredible houses. An absolute must for strolling around. Cow Hollow is similar, and close by.

In Napa, I would second the recommendation for V. Sattui. Beautiful winery; great place for a picnic. Also, go to one of the big wineries and take a tour; lots of fun.

St. Helena's a nice place to stay; very charming town. Napa (the city) is very sketchy and run down; I would altogether avoid it.