Alright, I looked each of the images I posted and using Google Earth found approximately where each location is in relation to the Golden Gate Bridge.

(Click for bigness)

Looks like They used the same CGI matte for Starfleet Academy in Voyager and Starfleet Command in DS9 (which may actually be a shot of the Academy, I've not seen the episode). It could be that Earth's Starfleet Command in Enterprise became Starfleet Academy after the Federation was formed. Both the Tram Station in TMP and "Headquarters" in TNG are on the city-side of the bridge. The only odd-balls out are JJ's Academy being on the city-side, and Command from Star Trek 4 is on the opposite side of the bay than where Command is in every other instance.

So:

Starfleet Command: Presidio/City side
Starfleet Academy: Sausalito side

Google Earth is a great tool to get an idea of what the bridge looks like from whatever angle.