Well, after having wake-on-lan running and working great (other than the stupid sleeping after a couple minutes issue) I decided I would do a quick post on how I got it working and my setup, it was actually very easy once I found the right package.
First, my overall setup. Linux/Ubuntu firewall, running iptables. 2 VLans, one for everything else. My desktop is on the client VLAN and the linux firewall acts as the gateway between both VLans and the internet.
My solution, SSH into the firewall