Now that I’ve purchased Duke Nukem 3D: Atomic Edition from GOG.com, I decided to dig out the Powerwave “PC USB Controller GP-036”… The only problem is, I can’t get the gamepad to work, despite the fact that Microsoft Windows’ Control Panel shows the gamepad as working fine! I tried playing around with the input setting for Duke Nukem 3D: Atomic Edition, however these appeared to have no effect?

Any suggestions before I send GOG.com an e-mail for some help?

I would use X-Padder for mapping the keys

http://www.dosbox.com/DOSBoxManual.html#Joystick
this link should help.

I think eDuke32 comes with gamepad support (although I don't know if it is only for xbox 360 controllers) plus a lot more. You should get it from the site.