The Atomic Edition of Duke Nukem 3D contains the three original episodes of the main game, the Plutonium Pak expansion, and many additional features like Windows themes, screensavers, jigsaw puzzles and an image carousel.
According to 3D Realms, Duke Nukem 3D: Atomic Edition is notable as being the first first-person shooter to include bots (AI controlled, human-like opponents).
In the "Duke Burger" Level, in the fourth episode, there is graffiti on the bathroom wall, that says "TRAB PU KCIP". Look in the mirror, and it will read "PICK UP BART". This is a nod to The Simpsons episode Brother From Another Planet.
References: Mission Impossible
The entire first level is a homage to the movie Mission Impossible. Here are some of the more obvious references.
The title ("It's Impossible!")
The music playing in the background.
Going to the desk and using the tape deck in the first room will cause the famous message "this tape will self destruct in..." to play. (Note: get out of the way fast, as the tape makes good on its promise)
In the briefing room, there is a coat hanger with a hat and cane on it which says "STEED"
The puzzle where you have to enter a code without touching the ground.
In the same room as the above puzzle, there is a garbage bin with greenish slime in it. In the movie, the computer operator gets drugged and ends up vomiting in a similar garbage bin.
Source code release
After many years of requests from fans, 3D Realms released the source code for Duke Nukem 3D: Atomic Edition (v1.5) on April 1, 2003. More information on where you can download it can be found on 3D Realms website: http://www.3drealms.com
Jonof's Duke Nukem 3D Port (A port using Duke Nukem 3D's source code that adds:
>OpenGL rendering support.
>True-colour textures support.
>Native Windows port using his Build engine port.
>MIDI playback and authentic sound mixing using ported >Apogee Sound System code.
>Experimental UDP-based multiplayer. )