You can try this, it depends on whether your network card in your FreeNAS system supports WOL.
You also need to make sure you have the plugin jail installed properly.
Open a shell prompt from the GUI and do:
Code:
jexec `jls jid` csh
pkg_add -rv wakeonlan
rehash
wakeonlan -i 192.168.1.255 00:aa:11:bb:22:cc
Replace the IP and MAC address with the ones for your windows system.
I haven't tested this, but it should work.
Don't try to install this outside the jail, it depends on perl and will probably fill up your flash drive and crash your system.