The computer on your bike has a fuel map, which is less complicated than it sounds. Think of it as a lookup table. The computer looks at the current state of the bike and how much throttle you're giving it and provides the amount of fuel that the table tells it to. A Power Commander or similar interrupts that signaling pathway and changes it, letting you effectively replace the default fuel map with a custom one. This can rectify lean conditions from the factory or due to modified intake/exhaust, and can correct certain fueling issues (like the snatchy throttle on our FZ6), usually at the cost of fuel economy. It can also increase power, but that's usually a lesser effect than the better throttle behavior or matching fuel to an altered air system.