SF is about the most expensive for hotels in the US but try Hotwire.com
I've gotten some really good deals for some great hotels. I'm only an hour from SF but I've stayed there several times at various hotels. Depending upon where you want to be in SF, one that I found surprisingly nice was Parc55. Very clean, nice staff, (not always the case in SF) and I had a great night sleep on a really comfortable bed. I got a great rate that averaged to $109/night YMMV