The 540 rpm speed for the PTO is the standard used for most tractors, although once you get over 90 horsepower or so, it is better to use 1000 rpm as the torque is cut in half and hence the drive line is not under so much stress. You can use 1000 rpm for running light implement such as linkage mounted spreaders and use lower eng rpm to drive them with small tractors. It is som times used for mowers to get the tip speed of the blades up.
usually when 1000 rpm is used, the pto shaft spline changes from 6 to 21 and then increases in size and changes to 20 splines on units of 180 + horsepower.
This is just to help maintain some safety in the drive line, it also saves the drive line in the implement as well (twisted shafts, hardening from gears etc). Mostly smaller units dont have enough power and inertia to keep a heavy implement spinning at 1000 rpm.
Hope this helps explain it better for you.
Cheers