Continuity Nod: The first mission with Hurk in the "Monkey see, Monkey BOOM" DLC stories involves stealing a stash of Bowa-Seko conflict diamonds from the pirates. True to form, they're represented by a single massive rock sitting in an empty briefcase, just like Far Cry 2.
A quest given by a man who believes he is being tormented by aliens asks you to find "their" packages for him. To track them down, he gives you the very same map-and-diamond-tracker device from Far Cry 2, albeit with the screen smashed so only the tracker works.
The use of plants as potent drugs to enhance human ability harkens back to Instincts, where Krieger's special "mutant" serum was made from similar herbs he found on the islands. Most of Carver's abilities in Instincts, including tracking targets by scent and greatly enhanced speed and jumping ability, can be replicated with the drugs you make from the plants on the island.
One side quest involves Seto, a secondary character from the game's Co-op story which takes place 6 months before the game proper.