Use the site that benvardboy mentions above, keep in mind a couple things:
- You simply download the client and unzip it, but there is one more step. You must take two files from your installed GOG version (or really, any version) of Duke Nukem 3D. The are called "DUKE.RTS" and "DUKE3D.GRP". Copy them to the root of the eduke folder (i.e. just copy those two files and paste them right into the "eduke32" folder created when you unzipped the eduke client). Then you just run the eduke32 application: you can even uninstall your old Duke3D version if you like.
- You may get some slowdown on Windows 7 and certain setups (AMD Radeons with their shitty OpenGL drivers) with the version linked on that site (I did, at any rate). Use the latest development build at http://dukeworld.duke4.net/eduke32/synthesis
/ and see if it fixes the problem, and there is a help forum at http://forums.duke4.net/forum/27-bug-reports-help-me-threads
It's a fantastic source port for a quality game, perfect for washing the bad taste of DNF out of your mouth.