There is a reference to Bioshock in the game. Hypodermic needles can be found around the island and the discription for a hypodermic needle reads, 'Filled with glowing liquid. If this were a failed underwater utopia, you wouldn't think twice about jamming this into your arm.' This is a reference to injecting needles filled with first aid fluid and EVE into your arm throughout Bioshock.
When Troy Baker auditioned to voice Pagan Min, he ignored the script and instead improvised a gruesome threat against one of the assistants.
The weapon A.J.M. 9 you can purchase with Uplay points is a nod to RoboCop. Aside from looks, The characters name in the movie is Alex J. Murphy.
The FBI/CIA agent that you meet, is actually the agent from Far Cry 3
The signature weapon HS77 is a nod to the Star Wars series. The weapon looks like Han Solo's blaster. It's name also contains Han Solo's initials "HS", and the year of "Star Wars: Episode IV - A New Hope" release, "1977"