The Wildcat armored car is illustrated by a picture of a Warthog from Halo. Grif complains that the vehicle looks more like a puma - a kind of wildcat.
One of the Orcs guarding the Towers of the Teeth muses "You ever wonder why we're here?" His friend then contemplates aloud how it's "one of life's great mysteries."
Infinity Train: Blossoming Trail: The Hidden Temple Car has numerous references like Chloe asking "Why are we here?" to which Atticus gives a speech asking about their place in the universe. They also assume that an adorable winged jaguar cub is a "chupa-thingy". Last, Chloe beats up some temple guards by channeling her inner Caboose.
Chloe: I'm Chloe Cerise and I. Hate. TEMPLE GUARDS!!!
Cortana attempts to alter her holographic avatar at one point to help disguise her appearance. One of the changes has her changing her avatar's color to pink. When the Master Chief points this out to her, Cortana responds by musing that she thought it was actually "lightish red."
At one point, Wrex calls shotgun on the Warthog, and N'tho says "Shotgun! Wort!"
The Mortal Son: In Chapter 12, two Orks have a conversation which apes the series' opening scene.
At one point, the Starks muse over the animal Theme Naming of UNSC vehicles and comment on the Warthog's lack the tusks of the creatures they are familiar with. They then state that the Warthogs actually share more similarities with the mountain lions (or pumas) native to the North.
One chapter begins with two members of the Night's Watch and two Wildlings basically re-enacting the "You ever wonder why we're here?" scene from the first episode of the series.
Literature
Halo: Glasslands: A Marine mentions that Sangheili just sounds like "Blarg! Honk!" to him. Additionally, the AI Black Box calls Evan Phillips "Phyllis", which was (supposedly) the original name of Sheila.
Video Games
Gears of War: There is an achievement entitled "Is it a Spider?", which is awarded for sticking 100 enemies with grenades in multiplayer (referencing the season 1 episode "Knock, Knock. Who's There? Pain").
There is even some delightfully recursive examples going back into Halo:
There is a rare line on the level "Outskirts", in Halo 2, where when under attack, a UNSC Marine will yell "I'll pull your skull right out of your head and beat you to death with it!" This is a reference to the Cruel and Unusual Death of Private Jimmy at the hands of Tex.
One of the notes on the flags used in the later games' "Capture the Flag" multiplayer sessions mentions that it is "right next to the headlight fluid."
In Halo: Reach, Elites will sometimes clearly yell "Blargh!" or "HONK!" when fatally wounded. Additionally, Emile (a member of Noble Team) seems to have been heavily inspired by the Meta in both their character design and personality.
In Halo 5: Guardians, the description for the HCS Contender Red weapon skins reads "Let's all take dying as an open action item", referencing a quote from Simmons in theSeason 2 finale "K.I.T. B.F.F.".
The Master Chief Collection version of Halo 2 includes an achievement called "Six pedals, four directions", which is unlocked by having the Arbiter drive a Scorpion. This is a reference to a line of Caboose's from the Blood Gulch Chronicles, where he asked why the tank had six pedals if there's only four directions (and referenced later in season 8, where we actually see a Warthog with six pedals).
Rooster Teeth's later show gen:LOCK had both lines of the famous opening line in separate episodes ("It's one of life's great mysteries, isn't it?" and "Do you ever wonder why we're here?").
The Nostalgia Critic plays the iconic sequence of Caboose killing Church for the first time in Season 1 and being proclaimed a Team Killer by Tucker during his review of Starship Troopers when there's an incident of friendly fire during a training simulation.
Honest Trailers both gave Halo the title Red vs. Blue: The Videogame and their recap of the 2022 Halo TV series concluded that viewers were better off watching the web series.
