When we think about the ancient days of id Software and the Commander Keen series, the first thing that comes to mind is the first historical reference to Quake, when this was the name of the character, not the game itself.
However, there is another, more subtle connection that many people overlook - the Standard Galactic Alphabet (SGA). It's a fictional language system that replaces English letters with "galactic" letters (the words are still normal words). And the funny thing is that one of these letters looks suspiciously similar to a familiar object from Quake.
Take a look at this screenshot (click to see ti larger) - the SGA sign says "POOL". Pay attention to the letter "O". Does it remind you of something? Something that you collect at the end of Episode 1 and which causes Chthon to emerge?
Another subtle similarity is that the objective of the first Keen game is to collect four ship parts, which is similar to the objective of Quake (collect the four Runes).