Hotel Whitcomb, avoid the snobs
Myself and my partner stayed here for our honeymoon. We could have spent twice the money and never left the room, but having never been to San Fran we wanted to enjoy the sights. The room itself is very comfortable and while not having a coffee maker in the room there is a Starbucks in the lobby for morning beverages. Free internet is a huge plus as well. While not in the heart of downtown the immediate access to public transportation right outside is an amazing convenience, unless your partner gets confused and swears that there's no subway to the Castro.
Would I stay here again, absolutely! I'm in San Fran for San Fran, not a flat screen TV and a coffee pot.