Shifting, or pulling, to one side under braking could be anything from sticky pads, seized caliper, worn suspension, tyre pressures, road surface....
Paullec's issue does sound like disc warp. Usually caused by Material Transfer as Kam325i says. That man knows his stuff!! If I have been 'ragging it' for a while, I don't even use my handbrake when I park up until the brakes have cooled (I live on level ground luckily!) for that very reason.
IMO, using the handbrake wont cause any pad transfer to the disk.. 80% of the brake force is directed to the front rotors so that's were the real heat is.
Material transfer only happens when your disks are extremely hot and you stop at the lights or something and hold your foot on the brake too hard.. most people keep a firm foot on the peddle at red lights.. you can take most of that pressure off, all you need is a enough to stop the car rolling.. so just a dab.. (once you've stopped that is!)
If you use performance pads, when bedding in, after each hard braking application you should never ever stop the car, always brake to about 10mph, release and accelerate and do it again.. that avoids uneven pad transfer and brake wobble. These pads rely on having an even lay of pad material transfered to the disk for proper performance.. what you want is an EVEN layer of material.. holding the brake on when you've stopped leaves a pad shaped extra layer of material on the disk, which then, over time, unevenly builds up causing that wobble you get.
In daily applications, under normal braking conditions, you can do what you want, they never get ot enough.. but if you thrash the brakes, avoid holding the pads on the disk until sufficient cooling..
The rear disks don't suffer from this.. unless I suppose you're on a race track..
hope this makes sense, i'm running out the door and wrote it in a hurry!