The story mission, Watchers On the Wall is a reference to the Night's Watch from A Song Of Ice and Fire/Game Of Thrones, Mario Frigo also urinates off the top of the wall, saying 'Ever since this wall came up I've wanted to urinate off of the top of it' referencing Tyrion Lannister, a character in Game of Thrones.
David Tennant voices himself as if he had been kidnapped by the general's men
If you go south of the town of Alba at night, there will be a D.J party, and the D.J is Bolo Santosi, one of the criminal faction leaders from Just Cause 2.
On the western side of the volcano island, skull island from King Kong is depicted in the cliff face
There is a doge mode where whenever you shoot someone or explode something text will appear like in the doge meme.