In a nutshell...
Consider the pulse width the power you're using to cut with. 100% pulse width on a 40W laser is the same as using 40W, 25% pulse width is the same as using a 10W laser. Even though it is truly on/off, the time between on/off is so fast that you can consider the power as being averaged.
Pulse rate is how often that averaged pulse fires. The pulse rate should be taken into account when determining the speed at which your head will be moving. Let's say you chose a 0.25 pps (pulse per second) rate and the gantry was moving at 1 ips (inch per second)... your cutline would be dashed, with 0.25" of cut followed by 0.75" of no cut, repeating. Although these are extreme values, it is actually quite useful in some circumstances such as cutting items from paper that you want left attached to the sheet (think perforations). Metals may want a high instantaneous heat pulse to make the actual cut, but a fairly low pulse rate to avoid heating surrounding metal. Some plastics will curl on the edge if average heat is too high, so you adjust accordingly. YMMV...
Hi-TecDesigns.com -- Automotive Lighting Systems