San Francisco Shops LBS
Road Rage - 1063 Folsom (@ 7th). Good prices on everyday bits, great service. Maybe the most track friendly store in the city.
American Cyclery - Stanyan & Haight. Everything you could ever want, lots of vintage stuff. Pricey but they can hook you up with almost anything.
http://fixedgear.americancyclery.com.
Refried Cycles - Haight @ Fillmore Lots of fixies, gets track frames in occasionally. Ex messenger.
http://www.refriedcycles.com/
Freewheel on Hayes - Travis seems to be able to get all the stuff that no-one else can. Co-op bike shop. The other store on Valencia has new frames and bikes (though sometimes an attitude).
http://www.thefreewheel.com/
Pedal Revolution - 3085 21st Street. Lots of 2nd hand bits, occasional fixie on the floor. Good service prices and they build a lot of street fixies for their customers.
http://www.pedalrevolution.com/
Saloon Des Bicilettes - Fillmore @ Haight. Small shop. A few bits, occassionally a frame or bike. But great service esp wrt to wheel building. Worth dropping by every now and then.
Also worth checking out the Bike Kitchen, Roaring Mouse and Big Swingin' Cycles.