In the 'Prototype Labs' Lost Expedition mission, when pressing the switch button, Jason will say "Would you kindly activate?", a reference to Bioshock.
Contributed by ProtoSnake
There is a section of the ocean where the water is missing, and the player is able to walk along the sea floor. The sea life, however, will swim through the air as if it were water.

Killing a jellyfish unlocks a Survival Guide entry that says "The screams through the night. The hot air of explosions shaking the treetops. The bodies. Some faceless. They were only following orders."
Contributed by Psychospacecow
After unlocking the south island, Willis will say to Jason, "This Russia operation has blown wide open. I'm joining Task Force 141, flying out tonight." This is a reference to Call of Duty: Modern Warfare 2, which contains a Task Force 141 group, who are tasked to find a Russian terrorist.
Contributed by DeerBoarDude
Alias Toufexis, voice actor for Adam Jensen in Deus Ex: Human Revolution, stated that he was originally the voice of Jason Brody. He worked on the role for 2 years, but after Deus Ex: Human Revolution was released during Far Cry 3's development, he was replaced. This was allegedly because the developers were nervous that anybody playing Far Cry 3 would think about Deus Ex: Human Revolution. Alias Toufexis has also said that he found this dismissal to be justified and understandable.
Contributed by Dazz
In the Lost Expeditions edition, the mission called "Ignition to the deep" contains several references to the Assassin's Creed series. You can find Abstergo's logo and a document about the pieces of Eden and genetic memory. The fact that Jason says "that symbol looks familiar" suggests that it is not just a Easter egg but that both Far Cry 3 and Assassin's Creed could takes place in the same world.
Contributed by Yoshikuni
To promote the game, Machinima shot a short web series called "The Far Cry Experience" starring Christopher Mintz-Plasse and Michael Mando as Vaas. This is referenced in the cover for the game. You can also find Chris's head in the sand in the game, which will get you the "Say Hi to the Internet" achievement.
Contributed by gamemaster1991
One of the main villans, Vaas Montenegro, shares more than just the voice of actor Michael Mando. Michael also contributed his likeness and motion capture work to developing the face of Far Cry 3.
Contributed by LaZrKaTz4109
There's a loot item named "Ripped Teddy Bear" which has the description:
An old teddy bear, eye missing and a musty smell. Stuffing is visible between the stitches. A worn, ripped label names the bear "Bo B-".

This is a reference to The Simpsons; Mr. Burns' childhood bear, Bo Bo, that was shown in the episode "Rosebud".
Contributed by DidYouKnowGaming