How much run-out can I have in a rotor before I start to feel it? I can't seem to find a spec in Bently's or elsewhere.

Sometimes I can feel a pulsing in the brake pedal, but I'm somewhat doubtful it's the rotors since it isn't very consistent; so I'd like to rule it out...

'04 Cooper S

 

^^ if its a rotor it'll get worse, and when it does it'll be shaking the whole car every time you hit the brakes, I had a nissan truck do it once.. it was a 97 at the time had about 89k on it.. like you it started off once in a while then later became very bad.

if you've not changed your rotors yet I'd pull them off and get them checked out.. on a machine.. sounds like you might have a small spot on just one and if caught early could be fixed. but if you wait you'll know for almost certain as I said.. a warped rotor starts to get worse pretty quick
It could be something else too.. glazed brake pad maybe? etc..

 

Generally a rotor should have less than 0.005" of runout (measured about 1/4" in on the rotor face..).

Hubs should be 0.001" or less. Always check hub runout when you have a brake pulsation concern.

Be sure to clean the hub face before measuring.

If its a "pedal up and down" feel chances are its brake rotor thickness variations.. If its a " brake and shake" with the wheel, it's a runout issue.