One of the films playing at the Murnau Cinema (aside from Zombies in the Snow) is titled Men in Beige. Barry Sonnenfeld, director of the first Men in Black film, also directed four episodes of Season the First.
In "The Miserable Mill Part 2," Mr. Quagmire tells the triplets they would have flunked eavesdropping at his school. Will Arnett was previously in Arrested Development, which features a school that teaches children to be as quiet and unobtrusive as possible.
In The Reptile Room: Part One, Count Olaf (disguised as Stephano) is briefly seen struggling to use a pair of chopsticks. This was a Running Gag for Neil Patrick Harris’ character, Barney, in How I Met Your Mother.
Count Olaf briefly takes over the freak show in the Carnivorous Carnival parts one and two. Neil Patrick Harris had a small supporting role as as prospective buyer for a traveling carnival in American Horror Story: Freak Show.
In "The Miserable Mill: Part 1" Lemony explains the meaning "out of the woods" and recalls how in Little Red Riding Hood, a wolf enters the woods and is menaced by a little girl. This is a nod to Patrick Warburton's role as the wolf in Hoodwinked!.