I also posted how to run SST TC with GOG's Duke3D in the mod thread, but here's the recap for you.
Download Starship Troopers TC
Site 1: http://www.duke4.net/ (Direct Link) -- 20 MB
How to run Starship Troopers TC in GOG Duke3D
1) Download SSTTC.ZIP and uncompress it somewhere.
2) Uncompress SST_FULL.DAT (with WinRaR, 7-zip etc.) in the Duke Nukem 3D directory, overwriting all files.
3) Uncompress SST_ATOM.DAT (again, with WinRaR, 7-zip etc.) with into the Duke Nukem 3D directory and overwrite all existing files.
Optional) Open up "dosboxDuke3D.conf" in NOTEPAD, scroll all the way down until you see the second last line saying "duke3d.exe", add "/XBOOT.CON" without the quotes after it (with a leading space, ie: "duke3d.exe /xboot.con") if you want to play the Boot Camp (training) mission.
5) Run Duke Nukem 3D from the Shortcut the GOG Installer created.
6) Have fun!
I also attached three screenshots so you can get a sneak preview what you're in for. SSTTC has some really innovative coding (for 1.5 standards), superb level design and an overall solid gameplay experience.