The short answer: Yes you can
I'm running Hayes calipers and levers with a set of aftermarket rotors and they work just fine. Just make sure you have the right size rotor for the caliper/mount that you have (ie. 160/180/200mm etc).
There are slight variances in the thickness of the rotors themselves (Shimano I think are slightly thinner than some), but this usually won't make much difference. It might just mean that you'll have to reset the pads before you can use the brakes that's all.
To reset the pads, you remove them from the calipers (simple job), and push the pistons back in using the flat of a spanner or something similar. Then pop the pads back in, stick the wheel in and give the brakes a squeeze for the pads to align themselves again.