San Francisco is one of those cities it's easy to fall in love with. This was not our first visit, so we skipped the typical. I would definitely NOT RECOMMEND anyone go to Fisherman's Wharf without the foreknowledge that it is a terrible tourist trap. We think it's hideous. But it may be for you if you like that kind of thing.
Here are some things I DO recommend:
Golden Gate Park: In winter, this is a lush, beautiful park. It’s marred slightly by the roads that dissect it.
Haight: Yes, it is touristy; no, it's got nothing to do with the Beats or the Hippies anymore, but it's still a fun place. There’s great shopping for punks and lots of very famous very good tattooists.
Sunset: Take the bus and go and see this strange part of town. It’s a kind of old people's seaside resort in the middle of SF, with a beautiful but polluted beach.
Take the cheap BART or CALTRAIN to some other parts of the Bay Area, especially Berkeley.
Take the bus. All except full-time hikers will need this after all those hills anyway, but it's cheap and fun although very bumpy. People will talk to you.
Walk as much as possible.
Japan Town is very interesting, with a nice cinema showing not the usual films.
Live music is great here; pick up the listings and take a chance with something.