Hitchcock and Scully's in-sync invitation to Jake ("Join us Jake... you know you want to... we're going to Wing Slutz") is inspired by the creepy twin girls in the classic, The Shining (1980).
While Jake and Charles attend the general store, they buy some items, including a magazine called Hot Rod. Andy Samberg starred in the movie Hot Rod (2007).
When Holt and Boyle confront Jake as he's attempting to clear out his desk, they tell him that the suspect was "picked up by the 2-7" based on information from Jake's files. The 27th precinct of the NYPD is the home of the long-running NBC police drama Law & Order (1990).
At Freedom Feast, Jake highlights a whole section of the table dedicated to Thanksgiving dinner, complete with turkey and stuffing, saying it was something he thought about a lot while in prison. Jake has previously displayed an utter lack of enthusiasm for all things Thanksgiving-related, stemming from abandonment issues having to do with his wayward father. He has, however, spent several Thanksgivings with his work family and has grown to appreciate it.