The Duke Nukem 3D: Megaton Edition game is a modest feature and graphics re-make of the Duke Nukem 3D: Atomic Edition, Duke It Out In D.C., Duke Caribbean: Life's a Beach, and Duke: Nuclear Winter titles. The Windows version has been out for a while on Steam while the Linux version is still evolving.
The latest beta of Duke Nukem 3D: Megaton Edition switches from SDL1 to SDL2 as a big all-around improvement. With the SDL2 switch, the developers have also added gamepad support to the Megaton Edition game. There's also some overlay issue fixes and other changes with this latest beta.
More details on this 1.4.0 Beta update can be found via the Steam Community.