If what you're describing is what I think it is, I occasionally get that on my disks after I've been for a run in the wet. I'm not sure but I think it might be a bit of light surface rust caused by moisture trapped between the pads and the disk - though it could equally be detritus from the pads themselves. I find it's easily removed with a cloth. Also, it'll disappear pretty quickly when you next apply the brakes.
On the other hand though, it could be worth checking your pads for wear, as evidenced by the depth (or lack) of grooves in the brake pads, and scoring on the disk.
[ This message was edited by: keef on 2006-12-14 04:54 ]