'The Shambalas' pamphlet - In Chapter 4: Bill's Town, among his magazines in his secret cellar, a pamphlet for a band known as "The Shambalas" can be found. This is a reference to the hidden city sought after by Nathan Drake in Uncharted 2: Among Thieves.
Uncharted 13newspaper - In Chapter 5: Pittsburgh, the player will come across a hotel. In one of the hotel rooms, a newspaper lies on the ground with a headline stating: "Uncharted 13: A Lush Movie — Justin Bieber as Drake." Drake refers to Nathan Drake from Uncharted.
O'Sullivan's bar - In Chapter 5: Pittsburgh, the bar found at the Pittsburgh bridge bears a striking resemblance to the pub in the opening of Uncharted 3: Drake's Deception. The name "O'Sullivan's" is also a reference to Nathan Drake's companion, Victor Sullivan.
Jak and Daxter plush toys - In Chapter 6: The Suburbs, the player will be able to enter a child's room right after meeting Henry and Sam. On a dresser, the player will be able to see Jak and Daxter plush toys.
Nathan Drake plush toy - In the same child's room as the Jak and Daxter plush toys, one can also see a Nathan Drake plush toy on the bed from Uncharted.
Naughty Dog mousepad - In Chapter 6: The Suburbs, the player will be able to enter another room after meeting Henry and Sam. In the room, on a computer desk, the player can find a blue mousepad with the Naughty Dog logo across it.
Uncharted board game - In Chapter 6: The Suburbs, the player will enter through a toy store. On a shelf in the toy store in the far end, the player will find an Uncharted board game.
Jak and Daxter board game - In the same toy store as the Uncharted board game, a player will find a Jak and Daxter board game on a shelf just to the left of the Uncharted board game.
Stress Cereal - In many parts of the game, including Chapter 7: Tommy's Dam and Chapter 6: The Suburbs, a box of cereal can be found, referencing "Trix" cereal. The name "Trix" is replaced with "Stress", and the cereal's mascot holds a glass of wine.
PlayStation 3 console - In Chapter 9: Lakeside Resort, upon escaping from David in the blizzard, the player can enter a store. Inside the store on a shelf near the windows, the player can find a PlayStation 3 console with two DualShock controllers.
PlayStation 3 console - In the Prologue: When the player goes down to the living room of Joel and Sarah's house, there is a PlayStation 3 on the shelf under the television set.
Naughty Dog clothing - Upon beating The Last of Us, the player can also unlock Naughty Dog clothing items for Ellie.
Uncharted theme - In an optional conversation, Ellie learns how to whistle a part of the Uncharted theme.
Eye chart - In Chapter 11: The Firefly Lab, there are eye charts with messages that can be read from left to right. One of them says "RUN YOU R NEARLY THERE DON'T QUIT!!"
Java Jak - A coffee cart in the O'Sullivan's pub is called "Java Jak." This is a reference to the Jak and Daxter franchise.
Faithful Dog - At the Lakeside resort, there is a pet store called "Faithful Dog". This is a reference to Naughty Dog, the creators of The Last of Us.
NDI Sticker - There is a NDI sticker identical to the ones seen in Uncharted 3: Drake's Deception on the wall of a bathroom stall in the Bus Depot.
Boat Note - In Chapter 6: The Suburbs, there is a note from a man named Ish who seems to be a fisherman. He could be a reference to the character Ishmael from Herman Melville's novel Moby-Dick.
The Game of "STRIFE" - In the season of fall, when Joel and Tommy are looking for Ellie on horseback, in the house you find her in there is a shelf in which a darker version of The Game of Life is found, depicted as The Game of STRIFE.
"Deadly fungus" newspaper - In the first chapter of Uncharted 3: Drake's Deception, on top of the bar table, the player can find a newspaper with a headline of "Scientists are still struggling to understand deadly fungus" which refers to cordyceps brain infection.
Tess is a reference to the girl named Tess from the Jak and Daxter series.
The Uncharted board game is a real-life board game by Naughty Dog.
The Easter egg of the "deadly fungus" newspaper added in Uncharted 3: Drake's Deception was said of being a "screw-up." When Naughty Dog added the Easter egg, they said that they expected to reveal The Last of Us before releasing Uncharted 3: Drake's Deception, although, they didn't, and they forgot about the game. They state how they almost spoiled the secrecy of The Last of Us themselves.
What some fans thought was an Easter egg was actually a phone sex line, however this was a mistake on Naughty Dog's part and therefore not an Easter egg.
It's possible that Marlene's clothes at the end of the game are deliberately similar to Elena's clothes from Uncharted: Drake's Fortune
Bill's Kukri is similar in appearance to Tenzin's kukri from Uncharted 2: Among Thieves
The name of the survivor group The Marauders in Factions reference a group of the same name in Jak 3.
In the art book, there is a picture of Chloe Frazer at the store in Pittsburgh.