Why would one want to do this since one may as well just run the game full screen? Well, I will tell one why one would want to do this.
I have to turn vsync on to eliminate jagged-edge artifacts that occur while panning from side to side. One of the downsides to doing this is a slight degree of mouse lag that, for me, renders the game almost unplayable. While playing Portal 2 a few weeks back, I learned that running the game windowed at 1920x1080 actually eliminated the mouse lag introduced by vsync. Not only that, you couldn't even tell it was running in windowed mode. I tested running Duke Nukem in windowed mode and, much to my delight, the mouse lag issue went away. However, Duke Nukem's max resolution while windowed is something like 1600x900 (if that's wrong, I'll edit this as soon as I get back from my next playing session).
If I could get this to run in a 1920x1080 window, I'd be one happy Duker.
Edit: I found system.ini and located the spot where it contains the window size and resolution, but it's all funky. In Notepad, there are spaces in between all the characters in the file. In Notepad2, there's a NUL. Editing this file in either text editor appears to corrupt it. Any ideas how to get around this?