What to do and what to eat in San Francisco?

So I'm going to San Francisco with my girlfriend because Ensiferum, Belphegor, The Absence and Amon Amarth have all decided to skip out on Phoenix. She wanted to go to and San Fran seemed like the best bet since neither of us have been there. We're going to be there for a week, during the last few days of September and the first week of October.

So besides the usual tourist trap sight seeing, is there anything underground I should look out for? We're gonna go to Alcatraz, Fisherman's Wharf, and she wants to see a drag show. I'd like to avoid as much tourist traps as possible and get away from shopping and such. We'll more than likely visit some museums and such. What good shit is there to do that is not well known? Also really good restaurants would be fantastic. Nothing too expensive i.e. under $100 for two people. All kinds of food is welcome.

Jam it back in, in the dark.