You can play the dosbox version using hamachi.
And if you feel like using command line arguments, you may play eduke32 using hamachi as well (or at least you should, I am about to try it myself): http://wiki.eduke32.com/wiki/Frequently_Asked_Questions
yep, it works, just tried it out myself.
Just use hamachi with eduke and use windows command line (hope you know how that works). When in the duke directory, use:
eduke32.exe HOST -net -n0:# (#=number of players)
and on the client side:
eduke32.exe JOINING -net -n0 192.168.1.1 (replace Ip with the hamachi IP from your host).