How much runout is acceptable in a disc brake rotor? I'm trying to sort out pad dragging / noises in Avid BB-7 mechanical disc brakes and I'm wondering how much runout in the rotor is acceptable? Right now I have about 0.05 mm (measured with a Park DT-3i).
0.05mm is nothing. Stop worrying about it. As long as rotor does not make noise or drags extensively on the pads, you'll be fine.

Rotors change shape every time you ride: you apply breaks a little longer than couple seconds, rotor heats up and expands, then cools down and shrinks. On extended periods of braking rotors can heat up enough to burn your fingers when you touch it (done it myself unfortunately). And when this level of temperature change is applied all sorts of transformation happens to the level of warping/runout. So you can spend all the time in the world to make rotor as true as possible, then you go for a ride and it all changed and rotor is nothing like you've left is last time when you fiddled with it.