If it's a steady clicking noise then it's probably a failing regulator/motor.
But if it's more of a snapping/cracking that's less frequent, it probably means there's a loose or broken bolt/rivet somewhere on the inside bracket. This usually only happens to coupes because of the weight of the larger windows.
My passenger window has been snapping for over a year and I'm too lazy to fix it. It snaps a couple times when I first put it up, then continues to do it for 4-5 miles when I hit bumps. But it still works fine.
