Hypocritical Humor: Kaiba tries to condemn Gozaburo for relying on a single monster to pull him through a duel. Gozaburo points out that Kaiba does the same thing all the time with his Blue Eyes.
Naked on Revival: When fusing with his father to ground them both in the Virtual World, Noah is... naked, for some reason.
Old Shame: After being sent back in time to the first episode, the characters immediately start in on how bad the audio and visual effects during the first few episodes of Yu-Gi-Oh! The Abridged Series were.
Squick: Yugi mistakenly thinks that he's trapped in "The Vagina Monologues" version of the first episode rather than the original, and ends up asking to see his grandfather's vagina rather than his card. Grandpa obliges.
Take That Me: Apparently spoofing the aforementioned Old Shame wasn't enough; the current episodes get plenty of flak as well.
Yugi: It looks like we're just going to have to keep repeating the same jokes that everyone got sick of ages ago until he sets us free!