The Halo series contains several shout-outs to one of Bungie's previous titles, Marathon, although some of these seem to be more a case of recycling phrases because they sound cool. Halo has MJOLNIR Mark VI battlesuits while Marathon has Mjolnir Mark IV cyborgs. Halo has Marathon-class cruisers. The Marathon Mission's crest has made its way into the Halo universe in several places, sometimes as canon and often as easter eggs — on the side of a ship, a robot's eye, and as an ancient alien race's symbol for humanity.
Halo 3 has a number of cameos from Sci-fi television, including "Sergeant Reynolds" (voiced by Nathan Fillion, who at one point gets to deliver the beginning of the quote on Big Damn Heroes) and a Marine voiced by Adam Baldwin shouting "Say hello to Vera!", along with Alan Tudyk delivering a very Wash-like speech "Tank beats everything". Katee Sakhoff appears from Battlestar Galactica to lend a voice to some of the female marines.
Someone at Bungie must love Firefly because the ODST expansion has Buck, voiced by Fillion, Dutch voice by Baldwin and Mickey voiced by Tudyk. Also characters will say 'Gorram that hurts' if shot enough. Another hilarious shout out is playing as Buck in firefight when throwing grenades he will sometimes shout, "This Is SPARTAA"
Actually, no, not someone. Everyone. Well, almost everyone. 99% of Bungie Employees are Firefly or Whedon Fanboys/Girls.
The principal actors of the Halo inspired machinima Red vs. Blue also appear, delivering an in-character exchange, the participants and contents of which vary by difficulty level.
The first game has several Alien references, including the calico cat Jonesy, "I have a bad feeling about this (drop)", "We're screwed, we're screwed man!"("We're fucked, we're totally fucked!", which got changed to "screwed" in the TV version), and of course, "Game over man, game over!"
The Master Chief is Spartan John-117. The protagonist of Demolition Man is John Spartan, Prisoner #117. Go figure.
The protagonist of Halo: Reach is designated "Noble Six", a reference to Alfred Tennyson's "The Charge of the Light Brigade", which refers to the titular brigade as the "Noble six hundred". It's also Foreshadowing, of course.
There's no doubt that Halo owes a lot to StarshipTroopers, what with it being about armored humans fighting aliens, but the ODST drop pods just confirm it—that's exactly how the Mobile Infantry deploys in Troopers.
In a Shout-Out to the series, Microsoft named their voice assistant app in Windows Phone 8.1 after Cortana. Originally it was just a codename, but after word got out, fans campaigned for it to be kept. Not only did they do just that, they brought in Jen Taylor to provide the voice.