Neighborhood in the city of, Cow Hollow.
City in greater Bay Area, Menlo Park.
Bernal Heights. Not a city, but I really don’t know what you want.
Not much of a city but my first thought is Alcatraz.
The Presidio.
Chinatown!
Sausalito.
Brisbane, then Basingstoke, then Scranton.
The first place that came to mind was the Mission District 
Noe Valley.
Yerba Buena
Haight Ashbury.
Proxima Centauri
Value City Furniture.
Sacrremento!
Outer Richmond
Tenderloin
Hunters Point?
Pacific Heights
I can’t believe that no one has mentioned Oakland or Berkeley yet.
Because they are cities outside of San Francisco? Of course, most of the answers aren’t cites in SF, but neighborhoods.