Putting a cheat code from episodes 4-6 and you'll get a message saying "Commander Keen is also available from Apogee but then, you already know that - right Cheatmeister?!"
The Vortigaunts are a clear reference to the Vorticons of the Commander Keen series, both in name and premise, as they are a peaceful raced enslaved by a malevolent entity who are forced to act as enemies.