A mechanic friend of mine always uses a dual action sander and a 3M scotch brite pad to make a cross hatch pattern on the face of the rotors. He said that the machine finish from the brake lathe didn't allow the pad to bed in correctly, thus not allowing the ideal interphase between the pad and rotor. I do this when I do the brakes on my cars. I always use OEM brake pads, whether it is on my Acura or Vette and scuff the rotors with a scotch brite pad and da sander. I also follow a bedding process for the pads and rotor of about 10 stops, increasing pedal pressure after each stop, and allowing everything to cool between stops. I've been doing this for a couple of years, and haven't had a squeek yet.
Brett