I built a new system including an ASUS P9X79 motherboard. Wake on LAN (WOL) was just not working for me, and a setting that would enable it did not seem to exist in the BIOS (well, the EFI). There's essentially no explicit documentation on how to enable this feature in the owner's manual. Online, I found many people struggling with the same problem on older ASUS motherboards: they seemed to fix the problem by enabling the Intel LAN PXE Boot ROM (LAN PXE OPROM)---this is not necessary! The PXE ROM is for booting over the LAN, not waking in response to a magic packet. There is also a distractor called ErP Ready which seems to enable more power features when the system is in a standby state, but also seems to be mutually exclusive of other power-on options.
The only setting you need to enable is Advanced \ APM \ Power On By PCIE/PCI. This makes sense because the Intel LAN controller is almost certainly connected as a PCIE or PCI device. I was able to wake the system from the off state using the wakeonlan program (a perl script) from MacPorts, even over WiFi.
