Having been going on since 2006, it's no surprise that some of the content from YGOTAS would wound up being even funnier thanks to future events.
- Season 3 features Noah as the head of 4Kids with the Big Five as his executives. Over the course of several months as these episodes aired, 4Kids was sued by TV Tokyo and Nihon Ad Systems (NAS) over their unauthorized usage of Yu-Gi-Oh! footage, a lawsuit that culminated with 4Kids losing the rights to Yu-Gi-Oh!, along with numerous other franchises, to the Konami subsidiary 4K Acquisition. The fallout from the lawsuit also forced 4Kids to declare bankruptcy and many of their executives were fired or moved around. The company reemerged in 2012 but officially shut down in 2017 after declaring bankruptcy again a year before. This all makes Season 3 absolutely hysterical as it features Noah totally unaware of what's going on in his company, including that they've lost the rights to Pokémon and One Piece, and eventually the heroes escape their base as it gets blown up with missiles.
- At one point, after he's shown the stone tablet depicting Priest Seto battling with the Pharaoh, Kaiba wonders if this means he and Yugi are destined to play card games for all eternity, and when Ishizu answers in the affirmative, he declares, "Best. Destiny. Ever." Come Yu-Gi-Oh! The Dark Side of Dimensions, Kaiba goes all the way into the afterlife itself just so he can settle his rivalry with Atem once and for all.
- Episode 27 has a brief moment where Tristan talks about card games on motorbikes. Couple months after the episode premiered, it was announced that Tristan's second VA, Greg Abbey, would be the voice of Yusei, the protagonist of 5Ds.
- "Stop trying to make 'BROOKLYN RAGE~!' into a Catchphrase. It's never going to work!" When you consider even Wayne Grayson loves using it in Joey's dub voice...
- Téa says "Oh, it is on in a manner similar to that of Donkey Kong!" during episode 49. About a month later, Nintendo copyrighted the phrase "on like Donkey Kong", making Téa's line sound like she's trying to dodge a copyright.
- The CardGamesFTW account was taken down due to claims of copyright infringement. In the episode posted just beforehand (50):Johnson: Your series is in violation of copyright law, it is my job to see that you are rightfully punished.
Joey: Hold on a second, you're that guy who's been taking out all the abridged series on Youtube! You're that guy who got us banned twice!
Johnson: That's right, Joseph. And you know what they say: third time's the charm. - The Take That! against Dreamworks in Episode 52, in which Kaiba calls Pixar movies vastly superior, ended up being poorly timed because a month after the episode's release, Dreamworks would release Kung Fu Panda 2 to much acclaim, while Pixar released Cars 2 two months after the episode, which was the studio's first critical flop and was panned as the kind of lame, uninspired animated movie starring B-list celebrities that LittleKuriboh accused Dreamworks of making.
- In the Leather Pants parody-of-a-parody Literal Pants,
Marik repeatedly takes jabs at Kirbopher's artistic skills when it came to animating the video. This becomes funny when you consider Kirbopher and LittleKuriboh's voice acting roles in the upcoming animation project Monster Boy, where they play a frustrated artist and a creature that exists solely to criticize him, respectively. - Mokuba's comment in one episode that, because his brother is Seto Kaiba, he can decide who lives and who dies. This becomes after Yu-Gi-Oh! The Dark Side of Dimensions, which implies that Kaiba basically owns the town of Domino and has his own security force. Meaning that Mokuba wasn't far off the truth.
- Concrete Giraffes ends with the Slender Man starring in his own movie. On watching it, Joey decides that Hollywood really is out of ideas. Cue Always Watching: A Marble Hornets Story being released in 2015, and Slender Man in 2018; the latter of which was negatively received, seemingly proving Joey's point.
- May be Harsher in Hindsight, depending on one's opinion, but episode 4 concludes with the promise of "New episodes every week". LittleKuriboh would become notorious for his constant schedule slips. Lampshaded when Melvin declares that statement to be his favorite joke of the whole series.
- The jokes early in the series about Bakura being a minor character, considering he would go on to become a Breakout Character, joining the Spotlight-Stealing Squad along with Marik, and being featured in a lot of the Abridged Series spinoff material.
- In Episode 40, Bakura says the forbidden word "Disney" during his duel with Yami, which is followed by the 4Kids executives showing up with the Imperial March playing in the background. Three years later, Lucasfilm would be sold to Disney, almost making the scene prophetic in a strange way.
- In one of the tie-in videos to promote a con, Yami claims Nowacking must be a lesbian for turning down his advances. Jess Nowack would come out twice since then — first as a lesbian in 2013, then as a trans man in 2018.
- Yami's memetic "Wait a minute, did you just summon a bunch of monsters in one turn? That's against the rules!" becomes even more hilarious after later Yu-Gi-Oh spin-offs introduced new mechanics that made summoning multiple monsters in a single turn possible:
- In ARC-V, that was pretty much the In-Universe reaction to Yuya inventing Pendulum Summoning, to the point where Yuya and his opponent could basically quote the exchange word-for-word.
- Yu-Gi-Oh! SEVENS introduces Rush Duels, one of the key mechanics of which is the ability to Normal Summon as many times as you want in one turn. Not only would what Yami accused Kaiba of now be perfectly legal, it's one of the main advertised features of the new format! Even better? One of the Rush Duel-legal cards used in early promos is the Blue-Eyes White Dragon!
- In the 2008 special "Seto Kaiba's Real Father", both Kaiba and the narrator wonder when Shenmue III will finally be released. The game would be announced in 2015 and was set to be released in 2017. Might fall into Harsher in Hindsight, considering the game got delayed for two more years.
- One episode ends with Marik and Florence singing "Stand By Me". Later, Final Fantasy XV was announced, and the game's theme is also a cover of "Stand By Me"... performed by Florence + the Machine.
- Mai Valentine's defining trait in this series is her giant rack, and she's voiced by LittleKuriboh for the first three seasons. In Season 4, she complains about how everyone only identifies her by that attribute. Season 4 has her voiced by an actual woman this time... a woman whose username is Boobs McBalrog.
- When Raphael took down the bridge in Episode 71, Yami calls him out on being Youtube. Three months after its debut, Youtube took down the video on the basis of copyright infringement. Once again, this may be Harsher in Hindsight depending on one's sense of humor.
- Kaiba's rant in the Abridged Movie about how he's the best character and deserves to win because he should be the real star of the show is even funnier considering that Yu-Gi-Oh! The Dark Side of Dimensions is not only Kaiba's Day in the Limelight, but it was originally intended to focus solely on him. Yugi and the others weren't planned to appear at all, and the film had to be rewritten once the producers changed their minds.
- Ishizu's line about having to solve a difficult Professor Layton puzzle may have been a mere throwaway joke, but then Yu-Gi-Oh! Duel Links had a skit featuring Ishizu inviting Odion to solve a Duel Puzzle, making her love of puzzles come off as Ascended Fanon.
- Kaiba's furious rant in Episode 72 when Yugi loses a card game to someone else sounds an awful lot like the Joker discovering that Batman doesn't consider him his arch nemesis in The LEGO Batman Movie.
- There is a Running Gag in which Kaiba tells Mokuba to shut up. Now in Yu-Gi-Oh! VRAINS we have a similar Running Gag with Yusaku telling Ai to shut up.
- The opening to Episode 71 has Yami take a shot at Ash Ketchum, stating that unlike Ash he's been able to win a tournament. As of the Alola series Yami can't make that contrast between himself and Ash anymore.
- Every Take That! against Yu-Gi-Oh! GX and Jaden becomes this in light of LittleKuriboh becoming a Converted Fanboy for them over the course of LittleKuriboh Watches YGO GX.
- There's a running joke on how big Seto Kaiba's ego is. There's also a running gag on how ultra-advanced Ancient Egypt is. In Yu-Gi-Oh! The Dark Side of Dimensions, Seto Kaiba’s Duel Links technology amplifies his ego to let him literally No-Sell the disintegration magic of the Quantum Cube, to the shock of the antagonists in that movie. In other words, Seto Kaiba's ego is so strong, he can stop Ancient Egyptian quantum physics magic.
- During the scene mocking the Singapore dub in Episode 54, the Pharaoh talks about him and Yugi riding skateboards. Guess what the characters do in Yu-Gi-Oh! VRAINS?
- "If history has proven anything, it’s that when a movie comes out and fans are upset about its content, Hollywood always pays attention to them and rectifies its mistakes!" Sure, Bakura was just being sarcastic as an extended Take That! toward the movie industry, but a couple of years later it actually happened! Twice!
- Mako's characterization as being in love with the ocean. In the second season of Yu-Gi-Oh! SEVENS, Yujin Goha is introduced, becoming a Man of the Sea overnight and introducing himself to the main characters by singing the sea a love ballad.
- In the Neon Genesis Evangelion one-shot, Shinji manages to curbstomp the Angel after being told to imagine it's his abusive parent. In The Suicide Squad, Polka-Dot Man goes through the exact same process to fight Starro and would have succeeded if he didn't get suddenly crushed.
- In Episode 73, Yami makes fun of Weevil for losing to someone that put Mushroom Man in his deck. Fast forward to 2022, and Mushroom Man #2 of all things is actually seeing play as a side deck option for Kashtira to deal with mirror matches.Why?
