The composer for both games, Gustavo Santaolalla, can be seen sat in a chair playing the theme on his banjo, just after you leave Ellie's and pet the dog.
The toy robot that Ellie gave to Sam in the original game can be seen in Ellie's room.
While riding through a winter landscape, Dina quips to Ellie that "You'll probably die from hypothermia from wearing canvas sneakers in the snow." which is what Ellie wore throughout the entire Winter section of the first game. Ellie clearly has a better wardrobe now though as she defensively tells Dina "I am wearing boots today".
Ellie's room at the beginning of the game has a PS3 (the console that the first game was released on) and games that appear to be Uncharted titles (a series made by Naughty Dog, the same studio as the Last of Us games)
The recurring guitar song that Joel first plays for Ellie in the prologue is called "Future Days" by Seattle-based band Pearl Jam. The album containing the song, "Lightning Bolt", was released October 11, 2013, two weeks after the outbreak of the Cordyceps infection in the game's universe, however the song was released a month beforehand on YouTube.