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I thought I remembered one besides Duke 1 & 2... maybe I'm wrong on this though
There's one for the Game Boy Color, which, if I recall correctly, is somewhat of a rehash of Duke Nukem 2. There was also one for phones. I don't think GOG's going to get either of those, though. :-p
Well, there is Manhattan Project (which is already on GOG.com) and that really is a 2D game as it is a sidescrolling platformed, just that it has 3D graphics and sometimes there is a corner that you go around and the screen shifts, but gameplay is purely 2D.

There is also Duke Nukem Critical Mass on the Nintendo DS which is similar to Manhattan Project in being a 2D sidescrolling platformer with 3D graphics, but it is a little different in that it has 3D arena bosses.
Duke Nukem Forever was originally supposed to be a side-scroller. I didn't think any screens existed, but I just saw them the other day here:
http://dukenukem.wikia.com/wiki/Category:Duke_Nukem_Forever_%28Sidescroller%29_images
this is what happened to the DN4ever engine it was sold to softdisk after being changed from an duke title.
http://www.mobygames.com/game/alien-rampage
the Duke nukem 1 games had the first engine witch was reused for math and word rescue. duke nukem II used an upgraded cosmo engine adding the elements fro the first game.
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SCPM: Duke Nukem Forever was originally supposed to be a side-scroller. I didn't think any screens existed, but I just saw them the other day here:
http://dukenukem.wikia.com/wiki/Category:Duke_Nukem_Forever_%28Sidescroller%29_images
That was a different game with the same name.