An unused placeholder character can be found in the coding of the arcade version of Continuum Shift 1. The character is named "Tubaki Yayoi" ("Tubaki" being a misromanization of "Tsubaki" as in "Tsubaki Yayoi", an actual character), her character select nametag is still written in the Calamity Trigger font and her main portrait is that of Nu's CT artwork with the head of Noel Vermillion's story portrait pasted on it.

In game her sprite is a static image of Nu/Lambda with "MU" written on it, meaning that Tubaki is aplaceholder for the character Mu-12, an alternate version of Noel.
Contributed by MightyKombat
In "Teach Me! Miss Litchi " Episode 1, Tao references the movie Pulp Fiction using Jules' famous reciting of Ezekiel 25:17.
Contributed by Naui
In various joke endings throughout the game's story mode, it is shown that protagonist Ragna the Bloodedge has a fear of ghosts. This could possibly be referring to ghosts being immune to Ragna's brutish attacks, which rely on physical weaponry. It also works as a reference to Ragna's rivalry with main antagonist Yuki Terumi, who had inflicted psychological damage to him as a child.
Contributed by TailsFiraga