Also, after brainwashing Film Brain into being the 4th Cloak, one of them makes a comment about how he will be bad for their image. If you are a hardcore Nostalgia Critic fan, you should know that this is a shout out to his "Old vs. New: Lord of the Rings" episode.
Spoony throws sacks of birdseed at the Cloaks while yelling, "2 magic! 2 magic!" This is the preferred alternative to actual fighting in the LARP system of NERO. When the Cloaks don't react, he then goes on to ask if they're using the Old World of Darkness system instead.
Word of God says it was to represent Gandalf's ring Narya the Great, the Elvish ring of Fire. Noah didn't want to wear the Red Lantern ring, and the Star Sappire was the next closest thing he had. (It eventually caused a lot of fan speculation about Gandalf's possible role in the finale since the image of Aeon in the flashback showed him wearing a pink ring as well. Noah cleared it up in the commentary.)
Larry Prince removes his glasses and puts them back on in homage to Walter Cronkite's reporting of John Kennedy's death. Which kinda makes sense considering the next thing he talks about after Jaffers' disappearance is the president being shot.
And, also considering that Jaffers' appearance now officially confirms the dating of the Critic's tape, Larry Prince now is referring to the Reagan assassination attempt in the 1980s.
Critic tells Linkara, "If I say no, would it matter?", a line Plucky Duck said in Tiny Toon Adventures, with the same timing and intonation.
Plus, his voice is an impression of Rick Moranis in the movie.
When the group encounters a guy watching TV in his basement, the sounds from the TV are the opening speech from Reefer Madness.
In Part 6, Benzaie's sword is hit by lightning, so he raises it to the sky and says "I have the power!"
One that seems to have gone unnoticed due to the in-universereactions to his Jareth costume, but when Jew Wario enters in costume, he apologises for being late as he was practicing his "Dance Magic" Dance.
Angry Joe's spanish guitar riff whenever he tries his My Name Is Inigo Montoya line comes straight from the Western episode of Red Dwarf, when the Cat introduces himself as "The Riviera Kid" and does a little dance.
Another Red Dwarf reference comes in the wake of Ma-Ti's death—Critic mentions that during his previous encounters with it, he had Groin Attacked death itself, a reference to Rimmer doing likewise in the Season 8 finale.
The animation was supposedly inspired by the animated scene from Harry Potter and the Deathly Hallows Part 1 telling "The Tale of Three Brothers".
Near the end Malachite proclaims that "The world of metal and wheels has come to an end." In Lord of the Rings, Saruman (the pro-technology wizard who joins Sauron) is described as having a mind of metal and wheels.
Much of the Running Gag involving Ma-Ti being tasked to do chores for the gang to keep him out of the way is a shout out to Secret Of NIMH when Mrs Brisby tries to keep Jeremy, a clumsy and somewhat useless crow out of the way when she needs to do an important task on her journey.