Perbacco
http://www.yelp.com/biz/perbacco-san-francisco is my favorite Italian place in the city. It's a bit upscale, but well worth it. (Probably need to make reservations way in advance)
Avoid driving if you can help it. BART is awesome and parking is a nightmare to find.
CF nailed most of the touristy things, but two I would add are the Cable Car museum on Nob Hill as well as the Presidio (Which can be easily integrated with a Golden Gate walk)
Sonoma>Napa>Marin
Oaktown has a lot of ty areas (around Oracle e.g.) but Jack London Square is awesome. Tons of places to eat.