Hardison & Parker show up looking suspiciously like Men in Black agents, black sunglasses and all. Later on, Hardison says, "You know the difference between us and them? We make this look good," which is a paraphrased version of the line from 'Men in Black': "You know what the difference is between you and me? I make this look GOOD."
"Willy Riker" is a variant of Jonathan Frakes' character William Riker from Star Trek: The Next Generation (1987) and subsequent Star Trek movies. Frakes, whose feature film directorial debut was Star Trek: First Contact (1996), is the director of this episode (as well as many others).
At 8:18 Parker pokes Eliot Spencer with one finger just as E.T. The Extra-Terrestrial poked young Elliott.
Eliot's undercover character Willy is based on one of Christian Kane's real life friends.
The "alien" signal that is heard in this episode is identical (or very similar) to alien rhythms heard in Star Trek: The Next Generation "Ménage à Troi (#3.24)". The rhythms were an important plot point for that episode.