Doom

This Edge Doom tarball includes software and OpenGL binaries. You'll need the SDL libraries and a doom2.wad or doom.wad file.

The binaries are hacked so that the intro screens display a little faster, and F12 is the default screenshot key.

ZDoom

ZDoom is an interesting project. It uses code from Ken Silverman's Build engine (of Duke3D fame), and supports scripts, proper 3D environments (including underwater), translucency and jumping. Unfortunately, there is no OpenGL version of Zdoom for Linux at the moment.

Download ZDoom-2.1.7.

GZDoom

GZDoom is an OpenGL port of ZDoom. It requires a 32 bit X-Server for GL graphics, but will fall back to software mode in 16 bit color. Unfortunately, this project isn't terribly well supported, and has many software dependancies.
Download GZDoom-lq-1.0

Doomsday (Doom, Hexen, Hereric)

Doomsday is an awesome project with stunning OpenGL and 3D effects. LinuxQuake.org does not host any binaries from this project, but at the Doomsday site you'll find lots of forums and downloads. Linux support is fairly good, and is well worth following the fairly complicated installation procedure ;>