An unused post-credits cutscene was discovered on a late beta build of the game dated to January 28, 2013, three months before the retail release. The cutscene re-contextualizes Far Cry 3: Blood Dragon as being "a game within a game", featuring a younger Vaas staring at TV static, and is seemingly connected to an achievement in the retail release titled "The Drug of the Nation". The achievement is unlocked by turning off all 32 TV sets throughout the game in order to "Decrypt the Hidden Message", though it's never revealed what this is. Prior to this discovery, some players theorized that the hidden message was actually telling players they wasted their time turning off TVs in a video game while staring at a TV expecting a reward, hence TVs being "the drug of the nation", and calling back to a popular monologue by Vaas from Far Cry 3 about the definition of insanity.

The 2023 Netflix animated series "Captain Laserhawk: Blood Dragon Remix", which is a loose adaptation of Far Cry 3's expansion game Blood Dragon (alongside featuring other recognizable Ubisoft characters), marks the first time that Rayman has ever been portrayed in an adult-oriented manner, featuring scenes with him saying swear words, drinking alcohol, snorting cocaine, and separately doing the latter while eating sushi off the back of a naked cow lady.

His flashback of going to college and then being rejected by humans due to being an alien is shown in a pixellated style resembling his appearance in the original Rayman while playing the song "The Lum King" from Rayman Origins.

Although it's not confirmed by Ubisoft, his story arc could be seen as an allegory for how Rayman's popularity dwindled since his initial debut in 1995.

During the final mission of the game, when Rex Spoiler:mounts the Battle Armored Dragon Assault Strike System the theme that plays is "War", composed by Vince DiCola for the film Rocky IV, which plays during Rocky's final fight with Ivan Drago.

The description of the Dragon Blade refers to the main protagonist of Assassin's Creed III, Connor Kenway, with the lines "There've been white ninjas and African-American ninjas and Luchadores, which are like Mexican ninjas. There's a Native American Assassin, can we talk about him?"

The city destroyed in the game's introduction has the skyline of Toronto, Ontario. This is likely a joke by Ubisoft Montreal, developers of the game, in reference to the "rivalry" between Montreal and Toronto.

The Galleria 1991 shotgun is based on the one used by the T-800 in T2: Judgement Day, and gets its name from the setting of the movie where the weapon is first used, and the year that the movie was released.

While visiting the promotional Blood Dragon website, entering the Konami Code (Up, Up, Down, Down, Left, Right, Left, Right, B, A) will change the mouse cursor into a targeting reticule, enabling for every component of the site be destroyed to reveal a picture of an Omega Force soldier.

The AJM 9 is based on the automatic pistol that Robocop uses in the film trilogy of the same name. The name itself is a reference to the title character's actual name: Alex J. Murphy. The idle animation for pulling out the weapon is Rex spinning it in his hand, a motion that Robocop became known for.

During the final mission of the game, the Spoiler:Battle Armored Dragon Assault Strike System exclaims "IMMA FIRING MAH LAZOR." This is a reference to an internet meme which of the exact same wording.

Towards the end of the game, after Rex Spoiler:picks up the Killstar, he will exclaim "I got the touch... I got the power..." This is a reference the 80's song "The Touch" by Stan Bush, made popular as the theme tune to the animated Transformers movie.

During the mission Summon The Plague, as the doors of the gate open, it will exclaim, "Test your might!" This is a reference to the Mortal Kombat series, which has a popular minigame of the same name.

Capturing the southeastern most garrison on the main island and taking on its hunting mission, you'll be sent into the sewers under the garrison to take out 4 pizza loving turtles. This mission is a reference to the Teenage Mutant Ninja Turtles.