Resurrected from r/streetwear. This info is 6 years old.
h&m, fatlace, almost any store on haight.
Not San Francisco, but Oaklandish has a store in Downtown Oakland at 1444 Broadway (between 14th and 15th). Worth checking out!
There's a mishka on mission now
black scale on haight
Bows and arrows in Berkeley is a little bit of a drive but it's tight. Wasteland in haigt ashbury too
FTC on Haight. Fiveone in Berkeley. It's a skate shop, but they carry a lot of HUF and other stuff. They usually get some of the more limited Janoski's, if you're into that sort of thing.
infinite SF - 627 Post St
UNDFTD - 516 Hayes Street
Darkside - 1827 Powell Street
MISTER / (Academy of Commons) - 1500 Grant Ave
Self Edge - 714 Valencia St
HAIGHT STREET (True, black scale, rvca, buncha thrift shops)