I've stayed around Union Square as it was convenient to the Convention Centre, head offices for companies I was meeting and major shops. Easy walk/cable car/BART/tram to Fishermans Wharf and everywhere else. Marriott, Nikko, Parc55 were all good. There was one at the end of Powell St near the cable car turntable that was very old which I don't remember the name of. SF hotels are usually pricy but on my last visit in August last year they were outrageous as it was the Flight event (air show etc). I ended up staying in Silicon Valley and catching the Caltrain each day.
Have you been before?