As in the title of the topic. I've been searching for the option in the menu + in the config files placed in Duke Nukem 3D catalogue, but i just can't find anythin'. Any suggestions?

setup.exe says it's not compatible with my version of Windows (64 bit Vista)...

Try setting the compatibility mode to XP on the setup file.

That didn't make any difference for me, still get the "not compatible, get a 64 bit one" message whenever I run setup on Windows 7 64bit.

So I poked about in the install folder a bit and found that there's a file called DUKE3D.CFG that contains the mappings for the controls. It's easy to read, says things like:
Look_Left = "Insert" "Kpad0"
So I just edited them in there with notepad (after backing up the file).

Go to the start menu and run the Setup file there. It uses DOSBox.

Look in the install folder. There's a shortcut called "Launch Settings". It will run settings in dosbox. It's much easier that tinkering with the .cfg file.
It'll even run on a 64-bit system.

Hey Guys.
I am also trying to change the controls in duke nukem 3d, and I red the comments in here and try them.
But I downloaded the game from gog.com and the only thing I can find om my computer is the game shortcut and the uninstall file. Cant get into the setup or install files.
What can I do now???

If I'm understanding you correctly, the only things you have found are the game shortcut (probably on your desktop) and the uninstall, but I may be wrong here because if you found the uninstall you should have found the primary DN3d install folder (and therefore found everything else, not just the uninstall). Just in case you, in fact, HAVEN'T found the primary folder, GOG's typical install path looks something like this:

C:\GOG Games\Duke Nukem 3d\