The five cards that go flying by are the Japanese versions of the five cards that make up the "Destiny Board" set from the Yu-Gi-Oh card game. In Japan, they spelled out D-E-A-T-H, instead of the English version's F-I-N-A-L.
The theme song has been replaced by Ave Satani, the song used for Bakura's entrances in "The Plot Thinnens". Lyrics were added by LittleKuriboh. A rock version plays over the end credits.
Bonz's expeletive subtitle "Frak!" is taken from Battlestar Galactica.
The part where zombie boy talks about zombies being replaced by the "The Infected" is a reference to the movie 28 Days Later and the Left 4 Dead games. Both have a legitimate excuse, however, as the Infected really are just living humans literally infected with a virus.
The stinger uses Kaiba's line seeing the giant rock from the original series, and bleeps out the word "rock", setting it up as an insult for what Kaiba is shown to be looking at, a poster of the live action Dragonball Z movie.
In the scene where the 4Kids Board Members are discussing about the prophecy, a clip of episode 128 of Pokémon can be seen in the background. That particular clip includes a hidden subliminal message against advertising, CEO Leo Burnett and 4Kids; when heard backwards, James says "Leo Burnett and 4Kids are the devil!" while he was trapped inside his Victreebel. Eric Stuart recorded this line in protest when he was told he wasn't being paid for his work in Pokemon merchandise commercials.