The de Young, SFMOMA, Yerba buena, and California Academy of Sciences are good spots for the GF. As someone else mentioned, Muir woods is worth the trip across the bridge if she's never been to a redwood forest. If you go, also go the the tourist club (if it's on the weekend). Sounds terrible, but it's really cool.
I like the Palace of the Legion of Honor as well; it's a little more remote but in a beautiful area of the city, close to the GG bridge. If you go to the de Young, Svpernaut, make sure you go up in the observation tower, which is free and separate from the whole ticket process. (You could just go there and skip the museum actually; I think the de Young is all hat, no cattle, but that's just me.)
Eaten there too....but I give Compagno's the edge. Maybe it's just me but my god they were good sandwiches
A few more suggestions for SF - drive up to Tomales Bay and shuck some oysters by the water. You get a gorgeous 1.5 hr drive thru Marin and fresh seafood that's an exquisite Northern California thing. Get drunk in the Mission and have one of the bacon wrapped hot dogs sold on the streets. lol. I love going to a Warriors game - crowd is awesome. See the view of the city from Mt. Sutro. Do a day hike around the Stinson Beach loop. Take the ferry to and from Sausalito. I like a place called Fish. Over there. The PCH is gorgeous from SF to Monterrey but not so great below that to LA. SF is a food town. try the cioppino, oysters, ice cream, fresh produce, etc if you can.
