Hotels:

Below are hotels that have gotten great reviews and/or have good price ranges. Some of them are in areas with cable cars—ask about getting a quiet room away from them!
www.sfguide.com/accommodations.htm (this link has some great pricing breakdowns for rooms per night)
www.argonauthotel.com
www.theorchardhotel.com
www.andrewshotel.com
www.carltonhotel.com
www.julianahotel.com
www.chancellorhotel.com
www.parc55hotel.com
http://sanfranciscoparkhyatt.com/gallery/sfoph/index.html

Lodging:
For those of you who might be interested in renting a house.
www.scenicrentals.com
www.vacationhomes.com
www.amsires.com/vacation.htm