In Level 7: Outpost, the hidden area where that level's Elysian Archive code can be found earns you an achievement called "Loekrise Kingdom". In that area, a small tent and clothesline are set up surrounding the code by a shoreline, with a message laid out in rocks along the shore that reads "LOEKRISE KINGDOM". This is believed to be a reference to the 2012 film "Moonrise Kingdom".
In several levels in the game, hidden areas with glowing blue codes can be found that could have been entered on a now-defunct website called Elysian Archives to access background story content, although each story page has since been preserved on the Internet Archive. Codes for each of the 8 archives can be found in Levels 1, 2, 4 through 8, and 10.
On the left side of the Biolab map, it's possible to find a soldier hanging from the edge of a ledge. He will say "Fly, you fools" and then fall, referencing a scene in The Lord of the Rings: The Fellowship of the Ring, in which Gandalf commands the fellowship to do the same.