Hi Brian. It depends on the part of SF in which you'd like to stay. On our last visit, we stayed in the Fisherman's Wharf area. It was touristy, yet convenient to the Muni, particularly the F-line that runs the vintage cars. We stayed in the Hilton Fisherman's Wharf, which was nice and very comfortable, yet not as nice as my usual Hilton (I'll get to that one in a bit). Several friends stayed at the Best Western Tuscan Inn near Fisherman's Wharf, and raved about it.
If you want to stay further downtown, you can look in the Union Square area. This is convenient to many Muni lines and a wider variety of restaurants. I usually stay in the Hilton located just outside Union Square when I travel for business, and there are many other hotels in the area.