A PS3 can be seen in The University, after you drop through the floor of the Dormitory to battle the Clickers and Bloater. It is in the room with the pool and foosball tables, sitting on the bottom of a bookshelf. Another PS3 is located in Lakeside Resort. While escaping from David's cronies in one of the stores a PS3 lays on the shelf. A PS3 can also be found in the opening segment when you're playing as Sarah, located in the family room under the TV.
While playing as Sarah in the prologue, when you walk into Joel's bedroom, look at the picture on the wall above his bed to see an image of a snowy forest with a lone deer in the foreground. This is an allusion to The Hunt section of the 9th chapter, Lakeside Resort, where you play as Ellie hunting down a buck for food, just before you meed David.
The movie theater seen early in the game is showing a movie titled Giraffic Park. Later on in the game, a classic scene from Jurrasic Park seems recreated to an extent with a giraffe in the university.
While in control of Ellie, in her backpack are 3 joke books. The last book, titled "To Get To The Other Side" with a picture of a chicken whistling, is written by Kathryn McCormack. This is a play on the name of The Road author Cormac McCarthy, as well as actress Catherine McCormack.
The first time the player controls Joel in the apocalyptic future after the title sequence, there is writing on one of the buildings to the left as the player progresses down the alley. The text reads: "SEEK THE FIRE", which is a reference to Cormac McCarthy's novel: The Road. In The Road, the father tells his son that they have to "carry the fire", which is a metaphor for keeping one's humanity, no matter how horrible the world around them becomes. This could have also been the genesis for the name of the "The Fireflys" resistance group that is trying to cure the outbreak.
During the Sewers chapter there are several notes to be found from a survivor named Ish. He is a reference to the 1949 novel Earth Abides by George R. Stewart, which tells the story of a post-apocalypse survivor named Isherwood Williams, more commonly referred to as Ish.
The Walking Dead
After exiting the sewers in Chaper Six: The Suburbs, you will find a sign that Henry will make note of. It says "Don't open, infected inside." This is a reference to the first episode of "The Walking Dead," where Rick attempts to escape the hospital but is blocked by a sign that states "Don't open, dead inside."
In the hospital during the final section of the game, there are eye charts on the wall. If you read them carefully, you'll see it's actually Naughy Dog giving some motivation to keep going as it reads: RUN YOU R NEARLY THERE DON'T QUIT!!
Naughty Dog series
Search the shelves in the ChooChoo Toys store to find "Jak and Daxter" and "Uncharted" board game, two other series from the developers of The Last Of Us.
During the Pittsburgh chapter you can find a poster about employee rights near the mob attack note. This poster is made by the JAK company, the phone number 1-800-555-TLOU, and the url for The Last of Us on it.
After meeting the duo of survivors after escaping the humvee during the Pittsburgh chapter, if you look in the kids/baby room of the same apartment you will find a pinata version of Jak and Daxter from Naughty Dog's previous series on PS2. In the same area, look onto the child's bed to find Nathan Drake, wise-cracking protagonist of the Uncharted series, in lovely plushy form.
Just after seeing Jak and Daxter and Nathan Drake you can spot them again in an abandoned toy store. Look closely at the shelves in the store to see both a Jak and Daxter board game and an Uncharted board game.
In one of the dorm rooms at the university you can see collectables you could come across throughout all three Uncharted games. These are difficult to spot if you aren't looking for them.
When you reach the part in chapter 5 where you, Ellie, Henry and Sam try climbing the ladder that breaks on the bus leading to the bridge, you will immediately come across an Irish Pub called "O'Sullivan's". This bar looks strangely familiar to Uncharted 3's opening bar segment. A coffee cart can be found called "Java Jak". Jack spelled "Jak" would be the main character in the Naughty Dog created Jak and Daxter games.
When you fall into the hotel basement and require a keycard to progress, notice the name of the person who previously owned the keycard. His name is "Jack Sullivinsky". Although Jack is spelled correctly, this could still be a reference from another Naughty Dog game called "Jak and Daxter". His last name could also be a reference to Victor Sullivan from the Uncharted series, as the first part of his last name is Sullivan spelled "Sullivin". He also appears to be wearing Sullivan's shirt from Uncharted: Drakes Fortune.
A Naughty Dog Logo mousepad can be seen in a kid's room on the Pittsburgh Chapter, below the room where you find the Jak and Daxter dolls.
Raja's Arcade is an arcade found in an abandoned mall in the Boston quarantine zone. It appears in issue two of The Last of Us: American Dreams. The name Raja is likely a reference to Naughty Dog's Uncharted franchise, which features characters named Eddy Raja and Rika Raja.