Step 1: Buy the game from the store or steam or whatever source you can.
Step 2: You need to install it with wine most likely, or dosbox if you have the old old cd. We will be getting back to this later.
Step 3: Get DarkPlaces. It is a high quality engine mod with great effects. As root:
equo install darkplaces
if you want the updated high resolution textures:
equo install quake1-textures
You can pick up some other cool addons for darkplaces from http://icculus.org/twilight/darkplaces/ if you want them.
Step 4: Copy your files from your installed windows version...
mkdir ~/.darkplaces cd ~/.darkplaces mkdir id1 cp /path/to/installed/quake/id1/*.PAK ~/.darkplaces/id1
For the last line, you want to ensure the proper directory for your installed quake, do not just copy/paste that last line.
Now you should be able to run quake with darkplaces just by typing darkplaces in a terminal, or you can make a launcher in gnome/kde/whatever.
Step 5: If you only want to play quake with none of the expansions, you are done, but if you have the mission packs, copy the rogue and hipnotic folders to the ~/.darkplaces folder. To launch the mods just run
To see darkplaces in action installed this way: http://www.youtube.com/watch?v=WNWwYcVp63g