Prboom

Doom 2 with prboom on Ubuntu

A Doom Port that runs natively on both Windows and Linux. It is even available through Ubuntu repositories. In order to actually play doom with it in linux, you must use the -iwad syntax with an appropriate .wad file.

WADS

The wad files come with the game if you purchased it. Otherwise, you could check DopeROMs and search for "Doom".