Happens elsewhere when Yami claims that Kaiba sounds like Brock from Pokémon.
Yami: "Screw the rules, I'm in love with Nurse Joy!"
Another Pokemon allusion: When Mokuba gets "Japanese Puberty", the first thing he says is "Bulbasaur!" That's because Tara Jayne did the first voice for Mokuba and Bulbasaur.
Yet another is made in episode 31. The little boy who thinks he's Ash from Pokemon is a reference to the fact Veronica Taylor voiced the same character...and didn't even bother changing the inflection she used for Ash whatsoever.
Variation in the redubbed Star Trek: The Next Generation opening spoof teaser in episode 32 - most of the characters get vaguely appropriate Abridged voices mapped to theirs, but Geordi Laforge gets Vocal Dissonance as he has the same voice as Serenity - a reference to them both being blind.
In the Episode 38 post credits gag, we see Howl doing Christian Bale's infamous on-set rant.
And then in Marik's Evil Council 3, Marik sends Dan Green to get Yugi's Millennium Puzzle.
In Episode 47, one of the Big Five, formerly voiced by GanXingba, claims that now that Yu-Gi-Oh Abridged is cancelled, children will have to make do with watching Avatar: The Last Airbender reruns for anime. When Kaiba points out that Avatar isn't an anime, he responds "It might as well be." GanXingba did Avatar: The Abridged Series, one of the most successful non-anime Abridged Series.
Inverted slightly In the Kami-con Season 4 promo video, Seto Kaiba mentions that Eric Stuart will be attending, and mentions only that he played Dr.Z from Dinosaur King and Brock from Pokemon. When prompted by Mokuba he also mentions Bastion from Yu-Gi-Oh GX.
During Season 3, Team Four Star voices the Big 5 (4Kids's group of executives responsible for cancelling the show in-universe). During one scene where Yugi and Joey are about to duel all of them, Gansley refers to all of them collectively as "Team Four Star," which Yugi corrects instantly.
Approval of God: Although the subject of many jokes in the series, the staff at 4Kids enjoyed it, and some elements of the series have become Shout Outs.
While some of the staff at 4Kids were known to have enjoyed the series, the original Japanese producers most definitely did not. LK once recounted a story of what happened when he met some of them at a convention and the translator told them who he was. The results were not pretty.
Ascended Fanon: Yami Bakura's name, Florence, was a joke used in Season 1 where he said his parents wanted to call him that. Eventually, Little Kuriboh decided to run with it.
Colbert Bump: A rather odd example. Prior to LK's abridged series, the franchise had started to slip off the radar. The abridged series ended up breathing new life into the fandom. 4Kids themselves seemed to have acknowledged this, even having Little Kuriboh join their voice actor panels during Conventions.
Creator's Favorite: Word of God says that Marik is his favourite character. Marik also has more appearances in side videos than other characters.
Incidentally, his least favourite is usually Téa, due to her voice being difficult to maintain.
In the flashback to young Marik's past, the Egyptian Merchant is voiced by Linkara.
Jaden in Bonds Beyond Time was voiced by ShadyVox, who was Jaden from Yu-Gi-Oh! GX: The Abridged Series. He also voiced him during two bonus episodes: his rap and his battle with Yugi.
Life Imitates Art: The series is cancelled by 4Kids in continuity and then it's taken off of YouTube in real life. This was right after the episode that featured Johnson/JudgeMan losing a trial against Joey, and then it goes back on YouTube just after the last episode defended it. Try not to think about that too hard.
Tristan[with original voice returned]: Hey, what gives? I liked my new voice! People were starting to take me seriously! Yami: Sorry, Tristan, but it's much easier to make fun of you this way.
The Big Five were initially voiced by LK, but are each by their own voice actor in The Cancelled Series.
Jaden first appears in the 2006 Christmas Special with Little Kuriboh doing a half-hearted impression of his dub voice to spout both of his actual catchphrases as part of a ploy to scare Kaiba. The next time he showed up, he was voiced by Shady.
Dartz was originally voiced by LittleKuriboh and had a voice not unlike Yami Yugi's; now voiced by Takahata101 with a voice like Coifio.
Talking to Himself: Prior to the cast expansion in Season 3, every single character in the show was performed by one man, with the exception of two incidental characters (Rebecca Hawkins and Gary Stu, both voiced by his now-ex-wife). He still plays the entire main cast, none of whom sound even remotely alike.