I don't think it is possible without spending hours upon hours on it.
Basically, for wake from lan, the machine only gets a signal to boot and that's it.
You can have two OS's and do whatever you want, but it will just boot in to the primary one or whatever your default time out action is.
Now - you can get a bit smarter - set the machine to boot from network then have a PXE server that has a script for your machines MAC address. You can then make a script or some program that switches this file based on your boot preference.
I know from experience that you can have a PXE server exit and boot from hard drive and boot from a linux kernel that resides on a TFTP server, so it would be easy to rotate these two options... however, I am not sure if it is possible to have a script that lists two seporate paritions on the same machine as when the exit command is given, it simply boots from hard drive as if by normal and it doesn't see anything else.
So, if you want to boot from hard drive (Windows) and have a Linux kernel over the network, I don't think this will be a problem - just time consuming.