Ryoko's for sushi near Union Square is open until 2 am every day of the week. Last call for food is 1:30 a.m.
http://www.ryokos.com/
Haven't been, but I saw it in an article a couple years ago, there's Toyose (Korean) out in the Outer SUNSET which is also open until 2:00 a.m.
http://www.yelp.com/biz/toyose-san-francisco
Someone mentioned Yuet Lee, which is also a pretty good choice. There are a couple Vietnamese places down the street from Yuet Lee (on Broadway, closer to Columbus) that I've also been meaning to check out. But not sure how "clean" you like your restaurants to look :-)