One terrific hotel to consider, just outside of town, is the Inn at Cavallo Point (on the Marin side of the Golden Gate); it's a spectacular setting (but you do have to drive to get into town). It's in the middle of what was an old army base, and the rooms are the former officers' quarters. Unique and definitely different.

Agree on the St Regis for quality, but -- the high floor Mandarin rooms, with the big window bathrooms looking north northwest towards the golden gate are spectacular . . .