The tires on the Warthog mention the name Puma. This is a reference to Season 1 Episode 2, when Grif says that he thinks the Warthog looks more like a Puma.
On Bungie.net, the Flag Kill and "Yoink!" medals both reference Red vs Blue. The description of Flag Kill mentions "It's right next to the headlight fluid," which is referencing Episodes 3 and 4 of RvB. When Red team tricks someone and steals something by surprise, they would say "Yoink!"
During Crow's Nest, if the player proceeds down a corridor, a marine can be seen knocking on a door asking for a password to be let in. On different difficulties there will be different conversations with different stars of Rooster Teeth.
In Halo: Reach some of the soldiers names in the Fireteam mechanic are the names of some of the people of Rooster Teeth.
During the level The Package, performing a special requirement allows the player to enter a special room called the Tribute Room, inside a database references Rooster Teeth and many other companies who have support Halo.
In certain episodes of Spartan Ops, there are hidden UNSC radios which, when shot, play Red vs. Blue's opening theme. As a result of triggering this easter egg, dialogue during key moments of a chapter will instead feature humorous dialogue voice by the series' cast. Finding one of these easter eggs will also award the Roses vs Violets achievement.