Melissa's attitude similar to Team Fortress 2's Sniper, with Ovaries.
The introduction to Mission 5.5 was one hell of a Metal Gear Solid shout out.
The name of Vincent's new “Deviance” chaingun is an obvious shoutout to the Firefly episode “Our Mrs. Reynolds”.
Vincent doesn't want an AI that sings stupid songs about cake.
John Morris, pilot extraordinaire, has a debilitating eye condition that requires him to wear perscription sunglasses at all times. This is similar to Jeff “Joker” Moreau from the Mass Effect series of videogames, who has a genetic disorder that causes his bones to break extremely easily - yet he's the best pilot in the Alliance Navy. (Also, John's speech explaining his condition in Interlude 4 is almost exactly the same as Joker's speech in Mass Effect 1.)
The Inflatable Crocodile incident is an in-joke with Luca (the author, not the character). Ask him about it.
“Come Get Some!” is a one liner from either Duke Nukem, or Army of Darkness, as is “It's time to kick arse and eat cake, and all that's left is pie!” from They Live (or Duke Nukem, depending on who you ask)
Vitriol's appearance is, as described informally by Luca (the author) “Like Sandslash, Vin Diesel, Venom and your maths teacher mixed together.”
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