Alternate endingThere is an alternate ending for this game. If you can get to the Secret Korath III Base, you'll find a fuse which can be broken by pogo-ing on it. Thus when the shikadi try to escape in the end, a different page appears that tells you their ship didn't start and they were arrested by the Korath III police for double parking.
DevelopmentEven though there is a Commander Keen 6: Aliens Ate My Baby Sitter!, Commander Keen 5: The Armageddon Machine was created after that one, because of the lead time required to launch at retail.
SwastikaAnother easter egg (but far more controversial) which can be found only on some versions is the representation of a swastika with pipes. This can be found on level 4 (go down the 1st pole, then left, then right after the short drop and finally look down (press down)) and was immediately deleted of all subsequent versions (although some say it resurfaced when GT re-released the series).
Information also contributed by John Romero, WildKard, xofdre and Zovni
Contributed by Tomer Gabel (4416) on Aug 15, 1999. [revised by : Patrick Bregger (98683)]. -- edit trivia