I've stayed at the downtown Marriott, Stanford Court and the Parc 55.
The Stanford Court is my least favorite - but those who like "old world" (think: stuffy and pretentious) may like it. An outside room, as one poster recommended, will get you a lot of street noise from those #$% cablecars. It is not very walkable to anything other than Grace Cathedral and the Mark Hopkins (it's the walk
back up those hills that will kill you
The downtown Marriott is pretty good and more convenient to the downtown area. As others have noted it is a big business hotel but my "tourist" stays have generally been pleasant.
I have grown to like the Parc 55. For transportation, the location is great since you are right next to all modes: BART, MUNI (subway and "F" trolley) and cablecar. The front side of the hotel is next to Union Square but the back side abuts the Tenderloin (best avoided at night). They seem to treat elite level guests well and the Concierge Lounge is pretty good. For location alone, this gets my nod.
Do a search for "San Francisco" on this board. A lot has already been written.