So i've had this issue for a little over 2 years now... ever since I've been using linux on my laptop. I used to dual-boot windows & linux on this laptop so i know it's not a hardware issue:

Windows Laptop waking Windows desktop (SUCCESS)
Linux Laptop waking Windows desktop (FAIL)

This has been with many different kernels, 3 or 4 different wol linux softwares, even just using netcat. The laptop has no firewall (iptables -L shows empty table and i don't have any other firewall software installed), windows machine has a hardware firewall but it's disabled in the bios (and anyways, it can be woken up from a windows machine).
I've even tried different network cards on the laptop (even though they all work fine when I booted it into windows).

If anyone could help me troubleshoot this I'd really appreciate it as there are times when it's very useful to be able to wol this box from my laptop.

Thank you

With the desktop computer running (obviously), try running wireshark or some other sniffer on it to see what packets are sent from the laptop, both under Windows and under Linux, when they are told to wakeup the desktop. (I hope these programs don't check first to make sure it isn't already awake, or at least have an option to suppress that test!) If you don't get any packets from Linux, use tcpdump under Linux to see if they are leaving the box.