At the end, the crew prank call Armus, the antagonist from Skin of Evil (1988), with Fred Tatasciore providing the character's voice. Both actors who originally played Armus, Mart McChesney and Ron Gans (voice), are deceased.
The Pakleds mistakenly refer to Captain Freeman as Captain Janeway, presumably because she is a female captain and Janeway is the most famous female captain in the Fleet (and the Star Trek franchise). Previously the Pakleds were shown to refer to any Starfleet vessel as the Enterprise, calling the Cerritos the Enterprise and, when the Titan arrived as backup in a fight, the Titan as "another Enterprise."
The crew members Boimier joins who are working on getting promotions call themselves the Red Shirts. In the OST the main uniforms were gold, and there was a running gag that anyone wearing a red shirt on an away mission would die.
Ensign Casey uses the phrase, "Excelsior." This is a Latin term that literally translates as "higher," though is generally used to mean forward progress in a positive direction. It is also sometimes used as a superlative to refer to items of good quality. The Excelsior is the name of one of the most famous ships in Star Trek, the USS Excelsior, fore-bearer of the Excelsior-class. Excelsior-class ships are one of the most plentiful ships in Starfleet, seen in 5 feature films and dozens of episodes of TNG and DS9. The catchphrase "Excelsior!" used in the way Casey exclaims it here, was also a popular utterance of Marvel Comics legend Stan Lee.
The USS Cerritos shirt that the Pakled spy gets from the gift shop uses the font of the original series Star Trek logo.