Off the top of my head, the Upper Haight has Wasteland, Held Over, Buffalo Exchange, and the Goodwill store (which often is ass, but occasionally has some good surprises). Aaardvark's is also there and might be worth a quick look, but has been crap for rather a long while.
And for incredibly pricey, save-up-for-months extremely splurgey vintage there's LaRosa's and a new place that's opened up almost right across the street from LaRosa's -- both are quite expensive but worth it: very beautiful (frequently couture) vintage stuff for both men and women, in excellent, wearable condition. Not for the bargain hunter, but great for vintage pieces you'll still feel happy about years later.
IIRC, there may be some more vintage and thrift in the Lower Haight, plus at least one good record store, and there's plenty of thrift and vintage all along Valencia Street in the neighborhood of the pirate store and Good Vibrations.
The Fillmore, Upper Market and the Castro I don't really know at all, unfortunately (I remember looking out the car or bus window and seeing some places but have no recollection of exact names or locations), but if someone else wants to lead the way I'm there.