I looked up to that older topic from 2009 and none of theses things worked :(
I went to the setup, I saved and started the game, but the controls remains the same! (I wanted to aim with my mouse and stuff)
So on I tried EDuke32, I open the file saying EDuke32 and it says.
"Duke Nukem 3D game data was not found. A valid copy of 'duke3d.grp' or other compatible data is needed to run EDuke32.

You can find 'duke3d.grp' in the............"
and I am using windows 7

If you want to change the controls in the original DOS version you could edit the duke.ini file. That's how I did it back in the day and that's what I did with the GOG release to change a few keys around.
The file should look strange to normal people, but for me that always was the easiest way to do that.

just use setup.exe to change the controls.

Yeah, this is really the easiest way. Just go through the files and click on setup.exe. Customize it however you want from there.

Just clicking on the file will not work on a 64 bit Windows. Use the link in the start menu.

Alright, total noob here. Is it possible to use a Xbox 360 controller and map the movement to the left and right thumb-sticks? Or even use more than 4 buttons?