The phase of the moon in the show was meant to match up with the phase of the moon on the night each episode originally aired.
There were originally supposed to be eighteen episodes.
In episode two, "Chapter 2: Hard Times at the Huskin' Bee", Gregory (Collin Dean), Wirt (Elijah Wood), and Beatrice (Melanie Lynskey) pass through Pottsfield, a town full of skeletons. This is a portmanteau of Potter's Field, a term for a graveyard for people who can not afford to buy a burial plot.
During the epilogue at the end of episode ten, "Chapter 10: The Unknown", Lorna (Shannyn Sossamon) can be seen reading a book called, "The Tome of the Unknown", which is also the name of the short story on which this mini-series was based.
All of the names that Gregory (Collin Dean) names his lucky frog (Jack Jones) are: Kitty, Wirt, Wirt, Jr., George Washington, Mr. President, Benjamin Franklin, Dr. Cucumber, Greg, Jr., Skipper, Ronald, and Jason Funderberker.