the debian user have blogged a short how-to on make wakeonlan work on your Debian box.
Read the guide here
Enter wakeonlan. Almost all newer hardware, especially those with onboard NICs (network interfaces), have the capability for that built in. So does for instance the Dell Optiplex GX620 I have here at work, as well as that shiny new LixSystems LX8100 with the Asus M2NPV-VM mainboard and a dual core AMD at home.