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Most implementations of the magic packet use UDP port 9 although this really does not matter as long as it is routed correctly and transmitted on the same broadcast domain as the target computer. So essentially it becomes a matter of getting a regular routable packet to the target host with the "magic" sequence inside its payload. The reason for this is the "magic" sequence can be anywhere within the payload. Yes the WOL magic packet is defined within the constrains of layer 2 but this does not mean it cannot be contained inside a network and transport protocol entity which can then be used to route it across the VPN. Old thread but I wanted to chime in because it is still the top rated search result for "wol over vpn".
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