Ooh. Anatorax is not talking about LED's. He is talking about the motherboard connector for the Power LED. That one spare pin is either connected one of the pins beside it or not corrected at all. And if you look closely at the case connector, I think that you will see that there are only two wires and the center pin is empty.
So, yes. You can change LED's. The simplest way is to use the existing leads and solder a new LED to the end of the wires and then mount it in the case.
Pyroflea, even most multicolored LED's have only two leads. What they do is put two different colored LED's in the same package and connect one backwards across the other. Then the direction of the current flow through the device determines which illuminates.http://www.scienceprog.com/bi-color-led-indication/