When Dipper recites the incantation to order Gruncle Stan's mind, the last are "Inceptus Nolanus overratus", an obvious reference to Christopher Nolan's "Inception" (2010).
David Lynch, director and creator of "Twin Peaks", one of the show's main influences, was offered the role of Bill Cipher. When Lynch turned it down, Alex Hirsch voiced Cipher using a bad impression of Lynch.
First appearance of Bill Cipher and Mabel's dream boys Xyler and Craz.
Closing credits music spoofs a song from an episode of Twin Peaks.