The Goodwill in the Haight Ashbury District is my favorite thrift store in all of the US. It has the best selection of vintage clothing of any thrift store that I have visited. It also has very reasonable prices.
There are also many other thrift shops with very reasonable prices in the district.
Vintage clothing shops abound in the Haight as well but are a bit more pricey.
The street is full of very special shops : second hand clothes from every style and year, hard rock shops, show clothes shops... Very funny to see even if you don' t want to buy!