Among the nicest places I visited in San Francisco was the future site of Starfleet just across the Golden Gate Bridge. It gives a really nice view of San Francisco and the Bay.
Well, one of Starfleet's future sites. We've seen Starfleet facilities on both sides of the bridge and elsewhere in the city. Ex Astris Scientia has a pretty good overview:
http://www.ex-astris-scientia.org/inconsistencies/starfleet_buildings.htm

It was really cold and windy, but my wife and I didn't care as this is such a special place in Trek to visit. I appreciate all the posts here that talked about visiting this and other Trek filming locations. We may try for some others down the line.