Treasure Island and West Oakland are some good places for lots of new apartment buildings.
I understand things are headed in the right direction over there, but I still wouldn't call West Oakland a "good" place for lots of new apartment buildings. Most people with any sort of alternative wouldn't even consider living there. Legal issues notwithstanding, from my point of view, most of the Presidio is an enormous waste of space in a city that is starved for real estate. If I were emperor, that's where I'd start in creating new housing for San Francisco.