Keen 5 Easter eggs
This is a list of easter eggs (intentionally hidden messages and functions) in Keen 5: The Armageddon Machine.
In level four (Energy Flow Systems), you can clearly see John Romero's name in the lower-right hand corner of the level. This is visible in the game (if you know where to look) and you can see it on the map picture. A swastika is also visible close by it, most likely a reference to Wolfenstein 3D, also by the authors of Commander Keen. (See below.)
The enemy name "Little Ampton" is actually far dirtier than it would first seem. Tom Hall says this:
Some British TV show referred to a guy with a... um, small... you know... as having a "Little Ampton". That stuck in my head when I was naming stuff, I guess. 
In Version 1.0 of Keen 5, in the Energy Flow Systems, there is a swastika above John Romero's name. However (probably due to public outcry), it was removed by Version 1.4. Here's what Romero himself had to say about the incident:
Tom Hall, creator of Commander Keen, further expanded on that point:
I think John put that in as a reference to Wolfenstein, not to imply anything about any character's ideology. Same as when he originally had the swastika shape in DOOM, that folks got so upset about that [he] took it out. As if that meant anything remotely like condoning the atrocities of Hitler. (Remember kids, Hitler bad. Hating groups of people for no reason, very bad. Killing people for the same no reason, very very very insanely bad.)
If Wolfenstein had had a logo, like a big "W" or something, then John would've made that shape, I'm sure. 
Extra Keen 5 Tune
There is an unused music track in Keen 5, that is only accessible by extracting the audio.ck5 data, or by creating a 16th level using TED5. However, if you directly warp to your custom 16th level, the game will crash because the Keen engine references a bad address of memory when trying to find the level name and entrance text. The only known way to workaround this is to "record a demo" of level 16 (F10+D) cheat, with music enabled, and listen. It is long enough not to be considered a place-holder.