According to this article in the Examiner Terrance Alan, in his role as a member of the Entertainment Commission, is once again trying to get the state legislature to change last call from 2AM to 4AM, a measure that was last considered in 2004. I think Terrance is completely right on this one when he says that the mass exodus of people from bars and clubs at 2Am is behind most of the noise and other complaints lodged against bars and clubs. Anybody who has rolled out of Drunk and Horny at 1.45 on a Saturday night knows about all the jacked-up people looking for something to do who then congregate on the sidewalk while they try to find out where the afterparty is. If bars closed at 4AM you'd have much more of a steady trickle between 1AM and 4AM, as Terrance points out, in addition to the fact that people tend to binge drink and emerge a lot more fucked up than if they were taking it in throughout the night (this was also confirmed by the British when they looked into extending closing times for pubs). Closing at 4AM would also alleviate the problems of cab hell that emerge when everybody is looking for a way home at the same time.
Also in the article, The Zebra Club in North Beach gets its license suspended after a deputy sheriff gets punched in the face, and the owner of Club 6 in SoMa (on 6th Street, one of the worst streets in SF), is issued a citation for noise.