Prboom

Doom 2 with prboom on Ubuntu

Prboom is a Doom port that runs natively on both Windows and Linux. It is even available through Ubuntu repositories.

WADs

The WAD files come with the game if you purchased it. Otherwise, you could find the file on DopeROMs.

Linux usage

In order to actually play it in Linux, you must use the -iwad syntax with an appropriate WAD file.