If you are on a Mac I'd recommend using the Fruitz of Dojo port. https://github.com/fruitz-of-dojo
While Tenebrae Quake is there you can just click Quake->Releases and download the .dmg for 1.2.1 - "Quakev1.2.1.dmg" mount it and copy its contents to a folder on your hard drive.
All you will need is the id1, rogue, and hipnotic folders present in the same folder. By default it will load id1. To load one of the missions packs drag and drop them on the GLQuake or Quake application as the read me says or use the CLI(command line tab) to add an argument to launch it(they'll be the first 2 options to add).
It comes in both GL and software renderers for Quake and Quakeworld and can play audio cd or MP3s in a folder of your choosing. Otherwise they are very bare bones and true to the original source as far as graphical options go. And it seems to work great on OS X 10.6.8 as well as 10.10.5.