The Dopefish has been featured in many video games, usually as an easter egg, including most Tom Hall and John Romero games, including all three Quakes, Daikatana (2000), Jazz Jackrabbit 2 (1998), Duke Nukem 3D (1996), and Return to Castle Wolfenstein (2001).
In the manual for the game, the description for the inchworms is that they'll be "afoot". If you collect 12 in one area (the only place you can do this is the Pyramid Of The Moon), they'll turn into the Giant foot from Monty Python's Flying Circus (1969) and take you to the secret area Pyramid Of The Secrets.
The green, one-eyed alien that Keen is revealed to have brought back with him from Mars at the end of Commander Keen 1: Marooned on Mars (1990) can be seen tied to a tree in the yard during the title crawl.
Secret of the Oracle's help menu contains an incomplete list of characters and their official descriptions. One of the characters listed is the Dopefish, whose description refers to him as the "second-dumbest creature in the universe", a reference to the Ravenous Bugblatter Beast, the "dumbest creature in the universe", in the Douglas Adams novel The Hitchhiker's Guide to the Galaxy.