"Life's a glitch, then you die" is a reference to the catchphrase "Life's a bitch, then you die." and the Year 2000 problem although it aired two months before it happened, because it was a prediction.
"Desperately Xeeking Xena" coined the term "A wizard did it".
Moe's phone call was a reference to the movie Scream referring to having a poor excuse for a plot hole.
Homer tells the guard of the rocket that he is the piano genius from the movie Shine and that his name is Shiney McShine (the name he should have used is David Helfgott).
The band playing at New Year's Rockin' Eve is actually Ratt according to the drumset, though the band members thought they were either Quiet Riot, Poison or Whitesnake.
Lisa being crushed by the bleacher with only her feet being shown is a reference to The Wizard of Oz when Dorothy's house crushes the wicked witch of the east.
In the third segment, Ned is wearing "Beatle Boots", which references that he was a fan of the Beatles before "The Bart of War".
This is one of two episodes of this season where the Simpsons accidentally run over a character, getting caught, and the victim turning out to be still alive. The other one being "Kill the Alligator and Run".
This is the ninth Treehouse of Horror to have the cast's names changed due to Halloween (e.g. Bat Groening). The first eight were from Treehouse of Horror episodes II-IX.
This is the first of two Treehouse of Horror episodes to feature the segment writer's name at the beginning of each segment, with Treehouse of Horror XI being the other.
Some of the names The Collector wishes for Lucy to name him on their wedding night are: Obi-wan, Iron Man, Mr. Mxyzptlk and Big Papa Smurf.
The way Ned writes "I know what you did" on the walls, it's a reference to Treehouse of Horror V when Homer wrote "No TV and no beer make Homer go crazy."
Marge reminds Bart and Lisa that they are vulnerable to kryptonite, the same weakness the DC Comics superhero Superman is vulnerable to.
The was the last Treehouse episode until XXIV to feature a Halloween Couch Gag.
According to the DVD commentary for this episode, Grampa was originally supposed to be the one run over by The Simpsons.
When Homer pokes the supposedly dead Flanders, he pokes him through the lenses of his spectacles.
If Lisa was excepted to escape from Earth and go to Mars, why didn't she get a letter? They could have left the house in such a hurry they didn't check the mailbox.
When the Simpsons were inspecting their roadkill you can see Flanders' sleeves intact. In the flashback story of Flanders when he finally caught up with the Simpsons after their car broke down, you can see that Flanders's sweater sleeves are ripped due to his lycanthropic metamorphosis.
Stretch Dude was able to punch through the collector's base wall, but only Clobber Girl has super strength.