- When Vaas orders Jason to start running away in the prologue, Vaas shouts after him, "Run Forrest, RUN!"
- Vaas's little dance when he's pouring lighter fluid around Jason and Liza is strongly reminiscent of Mr. Blonde's bit in Reservoir Dogs.
- Jason's reaction to hearing the name of Buck. "His name is Buck, and he likes to f-". Bonus points for both Bucks being scumbag rapists.
- Late in the game, Willis mentions he's joining Task Force 141 about a Russian operation.
- When saving Riley, he is forced to fly a helicopter, which he had not done before.
- Riley: I don't know what to do with this, man!
Jason: Use the Force!
- After the Story Mission titled "Dog Soldier", Jason jokingly requests to be killed if he starts showing symptoms of rabies. The quest-giver says "I'll buy a shotgun," and Jason laughs. He's probably seen the film... until he asks why you are laughing. Turns out he was serious.
- One of the saleable junk items is a ragged teddy bear missing one eye. It's labelled "Bo b-".
- One of the Lost Expedition missions has several.
- You can find an Abstergo logo on a wall and a letter mentioning "Pieces of Eden".
- When activating a power switch in the same mission, Jason will say "would you kindly activate?" in a faux Irish accent.
- When Jason sees the large old machinery he says "Hey Szalinski, you shrunk the kids."
- In the abandoned rocket silo complex, one portion has a number of jumping and platforming puzzles. Jason comments that he could use some kind of portal to help.
- The last of the memory cards talks about the potential market for Spice, mentioning one of its marketable applications as "interstellar travel."
- Another memory card mentions a new meth manufacturing method, which may help Hoyt's group compete with the "product coming out of New Mexico."
- One type of special arrow you can craft for the recurve bow is explosive-tipped.
- On one side mission, a character will refer to an odd incident as a "werewolf bar mitzvah."
- The title of one mission is cribbed directly from infamous gonzo "documentary" series Faces of Death. The title has a lot more relevance than you might think.
- This gem:Mercenary: At least they didn't send me to the island with the dinosaurs.
- When exploring ruins, Jason will come to an impassable stone door and say, "Come on Jason, channel Indy. Bet I can push that seal."
- In multiplayer, a "final move" taunt unlocked at level 34 is called "5 Finger Fillet", and holds the description "Hey, do the thing with the knife!".
- The last "final move" unlocked under the "merciful" category hints it involves dancing, and its description states "Admit it, you know all the moves." The move has the player free the hostage, and the two perform "The Macarena" together.
- The last "final move" unlocked under "violence" has the player pummel the hostage, before the player bends down and "teabags" the hostage.
- The first Hurk mission is called Dirty Diamonds.
- "Ride of the Valkyries" is a famous and revered piece of classical music in spite of its use in Apocalypse Now, but given the thematic similarities between the two pieces of work, it's safe to assume it's a reference to the film.
- The description for the traffic cone is "The hallmark of any good night out." Or, in other words: Hey, it's not a good night unless you get a traffic cone!
- Hoyt's mercenaries dress very much like the Canaries as well.
- In Far Cry: The Experience, when Vaas finds out that Christopher Mintz-Plasse is on the island, he picks up a radio and shouts, "McLovin. Is. HERE!"
- Vaas' "Definition of Insanity" quote is lifted from Rita Mae Brown. It is wrongly assumed to be coming from Albert Einstein.
- It's actually older, and comes from George Santayana. "Fanaticism consists in redoubling your efforts when you have forgotten your aim."
- The fight with Vaas seems like a love letter to Persona 4. There's a prominent TV motif, the fight is implied to take place inside Jason's mind, similar to how the Persona series in general takes place inside mental realms, and Vaas even says "I am you, and you are me", which is pretty close to "I am thou, thou art I".
Shout Out / Far Cry 3