When Abed and Rachel are watching TV and eating popcorn, the show playing is Rick and Morty (2013), creator Dan Harmon's other show.
You can see the bulletin board that needs to be replaced fall down in the second episode of the season Introduction to Teaching (2014) just before the protesting students enter the cafeteria.
Some of Chang's dialogue during "Bear Down for Mid-Terms" is taken directly from an e-mail Ken Jeong sent Dan Harmon, asking for a more serious role for his character.
In the previous episode, Chang mentions that his celebrity same-sex crush is Nathan Fillion. Nathan Fillion guest-stars in this episode.
When Annie yells "everything," this is a reference to Gary Oldman's crooked cop character yelling "everyone" from Léon: The Professional (1994).