We spent a week there almost 6 years ago...some of the things we did:
---We spent most of our time at a "bed and breakfast" style place. Studio apartment. It was nice because we didn't have to deal with the usual hotel crap (except for the last few days...they didn't have the place available for the full week). http://www.orangedogmanor.com/ Within walking distance of Golden Gate Park and Haight-Ashbury.
---We used the public transport (bus) most of the week. Worked out all right for us, once we figured out the bus lines.
---We rented a car for one day. It was the day we had to move to the hotel, and we used that day to go up North. Went to Muir Woods, hiked around, it was nice. We went from there to check out the Point Reyes lighthouse, but we had spent too much time at Muir Woods and the lighthouse was closing when we got there....
---We took the "Blue and Gold" Fleet (the ones that run the ferry to Alcatraz) tour of Napa. It was nice. Went to a vineyard (Viansa...nice wine and food!), an alembic brandy distillery (for a sniffing), and a "sparkling wine" vineyard.
---The Exploratorium is a cool inside thing to do, if you're into that type of thing.
---We actually used a guide, and had much better luck with restaurants that were recommended by the guide than when we "winged it." In particular, there was a narrow street that had a couple of bistros where they had tables out in the street, I believe it was in the Market District. Good food!
---Then of course there's the standard stuff you mentioned. Pay the extra for the audio tour of Alcatraz. It's worth it, IMO.