In Clementine's second flashback with Ava, if you choose to hum a song to AJ when he cries, the song she hums sounds relevant to "Alive Inside" from the first season.
First season to have two playable characters.
Javier was given a lifetime ban from baseball for betting on baseball games. This is a reference to the real-life Pete Rose, who suffered the same fate.
The voice actor of Clementine (Melissa Hutchison), is also the voice actor of Beauty and Toad Junior in Telltale's: The Wolf Among Us.