These are stuff I found on Yelp.

http://www.yelp.com/biz/mission-thrift-san-francisco

http://www.yelp.com/biz/thrift-town-san-francisco-2

http://www.yelp.com/biz/goodwill-industries-san-francisco-13

There is a Crossroads Trading Co. on haight st. and a ton of great shops all around it.

Out of the Closet at Church and Duboce is pretty cheap and has a good selection. Wasteland in the Haight has some good stuff but is pricey. Crossroad, Buffalo Exchange, Aardvark, and Heldover are decent in the Haight price wise and selection wise. Goodwill in the Haight is pretty cheap but kinda stanky and skanky.

Wasteland on upper Haight was always a good one; La Rosa is up there too; Thriftown on 17th/Mission; there’s some fancier thrift/vintage stores up the street on Valencia between 16th and 24th, too…

Buffalo Exchange on Valencia in the Mission always has good deals. Any anything in Haight.

WASTELAND! 1660 haight. totally #1.!!

here’s a good one: http://www.trazzler.com/trips/the-upper-haight-ashbury-in-san-francisco

As you may have guessed, all you really need to do is wander around Valencia street (near 16th) and Haight street (near Masonic).
I also highly recommend the goodwill on Fillmore at Post, and on South Van Ness at Mission.
Hope you have fun!