Try Dead Link Removed, which is right around the corner from SFMOMA, on Mission Street. They usually have an interesting show of contemporary photography.
The Avedon at SFMOMA is absolutely amazing, and there until 29. There's other great photography there at the moment.
49 Geary has quite a few small galleries with loads of great stuff. My particular favorite is Stephen Wirtz where I enjoy looking through drawers full of Michael Kenna prints.
There's also Fraenkel (sp?) in the same building.
Rayko on Third St. sometimes has great stuff.
If you have any questions feel free to PM me. Have a great trip!
Awesome info guys, thanks. I didn't know Avedon had a show going! The other shows and galleries I probably never would have found on my own. Thanks a lot. Keep them coming if there are others out there with ideas. Now if I can only get my wife to turn this into a pure photography trip!
I know it is a little out of the way but the Viewpoint Gallery in Sacramento is presenting an exhibit by Robert Glenn Ketchum opening on 11/13/09. Further details can be found at the gallery's website, viewpointgallery.org