During the side mission "Lost and Confused", Ajay will be given a drug by Yogi and Reggie called Oculus Spliff. This is a reference to the Oculus Rift virtual reality headset.
One of the game's side quests involves hunting down a rare honey badger called Gulo. This is a reference to a popular Youtube video called "The Crazy Nastyass Honey Badger".
There is a secret ending that can be achieved by waiting in Pagan Min's palace for 10 minutes after control is given to the player. Spoiler:During the scene, the player is supposed to try to escape and run away, but remaining in the area will have Min retrieve the player to join him, allowing the player to put his mother's ashes to rest, and then getting onto a helicopter as the song "Should I Stay Or Should I Go" by The Clash plays over the credits.