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".

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.

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.

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.

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.

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.

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."

In the 'Prototype Labs' Lost Expedition mission, when pressing the switch button, Jason will say "Would you kindly activate?", a reference to BioShock.

In the retail release, Dr. Earnhardt's backstory was very briefly acknowledged within his character entry in the Handbook, in which he sailed to the Rook Islands after his two-year old daughter died falling out of a window in their London flat. An unused cutscene left in the game files shows that Dr. Earnhardt would have personally revealed his backstory shortly after being introduced to Liza by Jason, following her rescue. Dr. Earnhardt specifies that installation work was being done, while in the retail release, no context is provided for how the tragedy occurred.

Found in the game's files are unused, fully completed animated narrative transitions containing thematically appropriate quotes from the Lewis Carroll novel "Alice's Adventures in Wonderland". While some of these were used in the final game, not all of them were.

Of note is that the unused quote pertaining to the "bottle" utilizes a subliminal-style visual effect with the quote which was recycled in the final game. The words "Drink Me" briefly flicker in order to state "Fuck Me", and when the narrative card cuts (as if to finish loading back into gameplay) it will very quickly flash into the words, "Kill You". The entire sequence would chronologically state: "Fuck Me, Drink Me, Kill You", foreshadowing the events of the "Join Citra" ending. In the retail version, the final quote transition used in the game states, "There is always a moral, if only you can find it." in which case, again, the word "find" will flicker into the word, "fuck", also foreshadowing that ending.

Evidently, the foreshadowing of Far Cry 3's "Bad Ending" was recycled in the retail version, possibly because of the original vision both being more direct and elaborate, as well as theoretically occurring much earlier in the story if implemented as is.