Merry Andrew and cjhsa pretty much summed it up. There are also some good places up at the top of California Street on Van Ness Avenue that are not bad places to stay and you can catch the Cable Car right on that corner that takes you down to Grant (Chinatown) and then further down to Downtown and then onto Fisherman's Wharf.
I was in heaven staying at a great little hotel on Sutter Street once though. It may have been called The Sutter Hotel in fact, if I remember correctly.
No matter where you stay it is going to be expensive. The public transit system is good and the Cable Cars are fabulous. You may want to just rent a car on days you do plan to travel outside of the City as most of what you need can be reached by PT or Cable Car as previously mentioned.
In any case, make sure your hotel has a concierge. They are the best at navigating you to wherever you want to go!
Oh, Chris! I wish I still lived there...I'd take you on all the personal tours you could handle! Just enjoy it my friend. I think it is the most beautiful City in the world!