'Mod's are modifications of the standard Quake game. Ordinarily you would have to use Quake's command line (accessed by holding the option key down as you launch Quake) and the Quake console every time you wanted to use these Quake variants. MacQFE replaces this process with a much simpler graphical interface that remembers your favourite settings and can launch them at the click of a mouse.
While using MacQFE is simple, it's not unsophisticated, and if you have more than a passing familiarity with the way Quake works then you will find that it can easily cope with the more esoteric needs of, say, GLQuake's transparency settings. Or, if you play Omicron BotBlasts you can set MacQFE to set up a blast using the required OmiExec file.