Golden Gate was amazing obviously. I think Twin Peaks probably had the best view in the city, though the site was a little trashy. I loved Alamo Square, though my wife was cursing me during the walk up to it (she's still recovering from a torn MCL). Loved the view from Battery Spencer as well. Sausalito, besides the view of the city across from the Bay had some awesome neighborhoods built into the mountainsides. Just about everywhere we went was amazing but probably top on the list would be Golden Gate, Muir Woods and the drive up Hwy 1 along the mountainside. Least favorite was Fisherman's Wharf and Chinatown. We didn't even get to those places till the last day. It was just too touristy. I got a better feel for San Francisco just walking the streets when we went for lunch and dinner; and we tried hard to find local hot spots that weren't tourist traps. I did enjoy the street performers on the Wharf though and Ghiradelli Square; that area seemed much more peaceful. And funny how we could count the number of food chains we saw on one hand our entire stay until we got to the Wharf.
Get a lamb shwarma at Truly Mediterranean. I know a few of them shut down, but I think there's still at least one in town. Those things are the bomb.