When I apply the brakes on my rover 600 I can feel a knocking in the brake pedal that can also be felt throughout the car. I changed the brake pads and one of the old set showed a little uneven wear. Should I replace the discs or should I be looking somewhere else for the fault?

When you did the brake job, did you grease the caliper pins with silicone caliper pin grease? Calipers need to move freely in-and-out, without binding, on the pins.

If you turned your discs, you may have lateral runout, where the disc(s) is (are) no longer at right angles to the spindle axis. In otherwords, they were ground to the cutting machine's axis, not the spindle's axis. If it looks like that's the problem, look into the Pro-Cut system for correcting the problem.