When visiting the councilwoman, Sam and Dean introduce themselves as "Special Agent Gabriel and Special Agent Collins". This is a reference to Peter Gabriel and Phil Collins of the band Genesis.
In a panel at C2E2 2016 with Robbie Thompson (the writer of this episode), he stated that in the bar scene with Good Charlie, Sam and Dean; that scene was originally written over 700 pages (according to the commentary on the DVD) to explain about everything that happened to Charlie in Oz and that in those pages, Charlie had a pet dragon named Mittens, which was written in as a joke.
When Sam and Dean confront Dark Charlie at the councilwoman's house, she says, "I should have known Rocket and Groot would track me down." Rocket and Groot are two of the main characters from the Marvel Comics series Guardians of the Galaxy.
Good Charlie is wearing a shirt that reads, "What Would Falkor Do?" Falkor is the name of the Luck Dragon in The NeverEnding Story (1984).
Sam makes the first reference in the series to the "Book of the Damned". He introduces it by showing Charlie a printout from the Italian Biblioteca Nazionale Centrale (National Central Library) with information on the actual Book of the Damned by author Charles Fort. This was Fort's first non-fiction book, concerning data that has been excluded ("damned") by mainstream science, including data on mysterious disappearances, UFOs, and other anomalistic phenomena.