In Far Cry 3, there are several hidden secrets referencing movies, games, jokes, famous people or events, also known as Easter Eggs.
On one of "The Lost Expeditions" levels, located near the centre of the map (x:-609.6,y:654.6), is an Assassin's Creed Easter egg.
Once starting up the mission, Jason Brody walks into a room and picks up a file folder. This folder has an Abstergo logo on it. Whilst playing through the mission, many more Abstergo logos can be found inside the compound.
Once finding all of the pieces to unlock a code, you are given a note from one of the inhabitants of the compound. This letter hints at Pieces of Eden trying to be uncovered and gives you the access code to the elevator. The code is 122112. This code can be decoded further, the 21st of December, 2012 is a Mayan prediction, but is the main event of Assassin's Creed Series involving Desmond (Main Character ) fighting templars to find the Pieces of Eden, and save the world from the date of 12/21/12, also known as the Apocalypse.
See video of the mission on the right:
In the mission “Aced in the Hole”, after losing a round of poker Hoyt says he will only remove one finger every time Jason loses and therefore removes Jason’s ring finger. This is a possible reference to how assassins would remove their ringfinger in the early days of the brotherhood as seen in Assassin’s Creed and Assassin’s Creed Origins.
In the "Prototype Labs" Lost Expedition mission, Jason utters the line "Would you kindly activate?" when throwing a switch.
At the coordinates (x:800, y:640) you will find a pirate on the beach dead, lying next to a boat. If you go out about 15–20ft into the water you can discover a pirate who is in a position in which his head is facing a toilet bowl. This is quite humorous (and ironic) as a pirate would need to stay on a boat for extended periods.
There is another sick pirate at the coordinates (x:769, y:681)(this time not underwater.). This is near a radio tower, in a building right next to it.
Say Hi to the Internet
Say Hi to the Internet is based on the promotional video "The Far Cry Experience". Upon finding the buried man in the sand (which although is a reference to Christopher Mintz-Plasse, the head in game looks like a member of the Rakyat), the action button will pop up to interact with the man's head.
There are two corpses hanging from a tree nearby.
Located around X:620 Y:559
After activating, the "Say Hi to the Internet" achievement/trophy will be awarded.
This is also the location featured on the game's cover art.
After killing Jason's brother, Grant, Vaas yells at the former, "Run, Forrest, run!" to Jason which is a famous recurring line in Forrest Gump.
One of the many loot items in the game includes a Ripped Teddy Bear. In the description it says the bear is missing an eye with a musty smell, has stuffing coming through the seams and a torn label reading "Bo B-". This is a reference to the Simpsons character Mr. Burns' childhood bear Bo Bo, who fits the description exactly and is a central plot item in the episode "Rosebud".
One of the collectible Memory Cards contains a formula for meth and a comment about how they hope "this compound will recapture some of the markets lost to the product coming out of New Mexico". This is probably a reference to the meth manufactured by the Breaking Bad character Walter White, who dominates the meth market and operates in New Mexico.
Another one of the collectible Memory Cards contains instructions on synthesizing a drug called Spice. One of the side effects listed for the drug is interstellar travel, a property shared by the Spice featured in the book Dune.
During the briefing for the side mission "Home Delivered" an NPC says, "Lots of spooky scary stuff, like a werewolf Bar Mitzvah". This is a reference to the music video "Werewolf Bar Mitzvah" by fictional character Tracy Jordon shown in the episode "Jack Gets in the Game".
Previous Far Cry games
There is a lady in a rocking chair outside of the Badtown gun shop. When spoken to, she expresses her belief that she is one of the several people who resemble all characters from the previous Far Cry games.
There is an item in the game called Conflict Diamond referring to the diamonds in Far Cry 2. There's also a side mission where you get to use the handheld GPS of Far Cry 2 (used to locate nearby diamonds in FC2) but the screen is broken in FC3.
There's also another reference to Far Cry 2. In the description for the master difficulty, saying that it is "worse than malaria," a reference to the infamous malaria mechanic in Far Cry 2.
In the mission "The Medusa's Call", Jason have to access the pirates' communications network situated in a beached vessel named "Medusa". This is the name of the boat used by Jack Carver and Valerie Constantin (the two main characters of Far Cry 1) to reach the island of Dr. Krieger.
On one of "The Lost Expeditions" located at X:530 Y:775,4 Jason says "You know, I could really use a portal right now." while climbing up the side of the Rocket Chamber.
Too much video games
There are warnings on numerous objects, such as just under the handlebar of Jet Ski's, which say "CAUTION Playing too much video games may lead to aggressive behavior. Handle with care. Herp derp."
This message appears in various other locations including on the alarms for outposts.
Jurassic Park reference
Star Wars Reference
At the end of the mission Betting Against the House when Riley tells Jason that he doesn't know how to pilot helicopters, Jason replies with "Use the force", a reference to the movie Star Wars Episode IV: A New Hope.