Have tea in the Japanese tea garden in Golden Gate Park. Have your photo taken by the Golden Gate Bridge. Book a tour of Alcatraz, the prison island out in San Francisco bay, go by night if you really want to savour the atmosphere of the prison. Take a ride on a cable car from Union Square to Fisherman's Wharf, where you can see the sealions and seals playing in the bay. For upmarket, individual shops go to the Marina district.
Fishermans Wharf / Pier 39 have good restaurants. No one has mentioned Lombard Street, the crookedest street in the world, walk to the top or have a drink in the cafe at the bottom of the hill. Winchester House museum, the residence with the most rooms. The trolleys & the trams.
Pier 39 looked like Great Yarmouth to me, nice though. No-one's mentioned Haight Ashbury, the old hippie district. It's pretty commercial these days but has some good shops and sights.