I've got a 12.04 headless server that I've been trying to get to work with wake-on-lan. The card is Marvel 88E8053 using the sky2 module. Although WOL is enabled in BIOS and ethtool shows the card as WOL enabled, it refuses to wake when I send the magic packet. I have verified that the packet is being received OK when the machine is on. The machine does wake OK from a BIOS alarm which suggests it is a network card issue.
I've seen reference to bugs in sky2 that mean WOL fails in recent versions of Ubuntu (and have tried a module conf file as suggested here but to no avail)
So I am thinking the best bet is to replace the ethernet card with one that definitely works with WOL in 12.04 - please could you post your card make and model no if you are using it successfully, along with any tweaks you had to make?