I just stayed at the "W" a couple of weeks ago and really liked it. It will be my new SFO 1st choice!
My previous favorite was the Marriott - You have to love the architecture, it is by far the most interesting building downtown. Sure the rooms are nothing special, but that is what I like about Marriott, they are consistant. And the View Lounge is awesome, as well as the location at Yerba Buena Gardens.