In the Matrix-style sequence when both Cass and Leo run out of ideas to thwart the Meech, the choir in the background sings "Do or do not - there is no try", originally a line from Yoda spoken to Luke Skywalker.
In he recollection of Leo's instructions regarding the intricacies of the game, Cass explicitly re-imagines them as an homage to th Matrix training sequence.
(Extended version only) When Joanna pushes back the 501st Legion security in the True Dungeon, she quotes Gandalf in his fight against the Balrog ("You shall not pass!" - "Fly, you fool(s)!").
As a part of the Ninja Dragon Riders theme, Gary sings "... you can't take the sky from me." Theme song from another cancelled (AKA fireflied) TV show.