Actor Allusion: Thinking back to when Yusei ordered milk at a bar, guess who else did the same in the music video of RUN&GUN's "Believe"?
Anime First: While the original Yu-Gi-Oh! (and now ZeXal too) had a manga before the anime, 5D's took the GX route and did not get one until over a year after the anime premiered.
Bad Export for You: Present in the Tag Force games, which removes the voiced content and has glitches not present in the Japanese version (such as in Tag Force 5 the Machine Emperor's summoning cinematics won't register in the photo gallery).
Fan Nickname: Probably the most famous is 'Crabhead' or the phonetic "Yousay" for "Yuusei," although nearly every character has one, as do some inanimate objects and plot devices. See its section on the Fan Nickname page for more.
And the fact that an insert song is called Yousay may or may not be a Shout-Out to the fan name.
Some people called out Aki as Kallen for their similar appearance.
Game Sue and Hat Guy for the main character of the various games because he usually takes the place of an established character (such as Crow in Over the Nexus) and sidelines the rest so that you can be the one to beat the bad guy.
I Knew It: One of the many Epileptic Trees surrounding the Tenors, and was recently revealed to be true in the anime, was that the three are the same being, each of them representing a period in the life of the same person. They are, and they do, and that person is Aporia.
Keep Circulating the Tapes: For the dub version, since 4kids lost the license to it. Thanks in part to no DVD dubbed releases outside of a few Australian DVDs and the online streaming episodes at Toonzai and Hulu that may be removed.
Jossed: A rather memorable one was the popular theory about Rex being the Fifth Signer. Jossed in episode 57 when it was confirmed that his brother, Rudger originally had the Head mark.
Interestingly, the joss doesn't last long, as Rex takes on the Head for himself in Episode 62.
Along with the other birthmarks!
The more epic joss came much later when ZONE's identity is revealed to be a random scientist guy who took on Yusei's image, not Yusei himself. Fans were bitter.
Marth Debuted in Smash Bros.: In America, Reverse of Arcadia, one of the video games that roughly follows the entire Dark Signer arc was released before the last four episodes of said arc were dubbed. This spoils Divine's second death, Rex becoming a dual Signer, and the entire DS finale for dub watchers. Oops.
Not to mention the Heart birthmark, which Rua would receive over a year later in Episode 142.
Dark Signer Godwin appeared in WC 2010 months before he did for the english anime, as well as a few minor characters in early season 3. The same goes for Crashtown!Kiryu and Tag Force 5.
No Export for You: The OVA, which debuted the game's new Buster(Assault Mode in the TCG) cards.
4Kids has now chosen to skip dubbing episodes 111-122, and to not dub any episodes after 136, so they can move on to Yu-Gi-Oh! ZEXAL. This leaves a lot of questions unanswered, such as the identity of the being who gave Yusei Shooting Star Dragon, and what the Divine Temple (Ark Cradle in the Japanese version) actually is. The prior episode skipping also means Jack simply pulls Red Nova Dragon out of his ass with no explanation during the duel with Team Ragnarok.
Luckily, 4Kids has indicated they will release the undubbed episodes subtitled on Hulu.
Tag Force 6 debuted waaay back in 2011. Neither hide nor hair has been seen of an English release.
Screwed By Network Collapse: While the original Japanese airings avoid this, getting the same timeslot and never going on hiatus currently in its run, the dubbed American airings aren't so lucky. First appearing on the CW Saturday morning block, it's timeslots constantly changed around, airing as early as 7am or as late as almost noon. It also went on hiatuses often, and refusing to air certain episodes due to content. Finally CW stopped airing it since DM proved to get better ratings. 5D's did a Channel Hop to Cartoon Network, but its problems haven't ended yet. Now episodes air at 8am on weekdays, a time when most of target audience is attending school. New episodes update randomly and one must check the 4kids website to find the latest episodes. Oh and streaming episodes are only available for Americans.
Now that 8AM timeslot is reserved for reruns for Pokémon. Back to the CW.
Due to a major lawsuit filed by TV Tokyo and Nihon Ad Systems for a debt exceeding $4.5 million, 4Kids had to stop the dubbing process in its tracks and file bankruptcy. It's a rare, wild case where a network didn't exactly screw the program- they lost the rights and resources to air it.
The Other Darrin: Carly's VA from 130 onwards was replaced due to an unrelated issue that caused her to quit. In the English Dub, Rex received a new voice from episode 15 onwards, because of the tragic death of his VA, Maddie Blaustein, and Crow's voice switched to Tom Wayland from Pete Capella starting in episode 92.
Too Soon: The tornadoes Placido created in his duel with Yusei are completely absent in the dub, due to the recent torndoes disaster in the Midwest.
What Could Have Been: In Takahashi's original design notes for Crow, he's more of a Team Rocket figure, described as constantly trying to steal Yuusei's D-Wheel and always failing, eventually befriending Yuusei at some point.
To add to the above, one of the writers have confirmed that Crow was intended to be the final boss of the Dark Signer arc.
Also Mukuro Enjo, who apparently was a teammate of Yusei and Aki and won the Pegasus J. Crawford Cup Trinidad Riding Duel Grand Prix with them in Z-One's original timeline!
In-universe. Z-one's computer terminal in Episode 149 lists information about Yusei and his friends that tease before he messed with the timeline, things went quite differently. Significant changes include only five Dark Signers, Yusei and Aki teaming with Mukuro Enjo/Hunter Pace to win a tournament, and Yusei having a new ace monster, "Cosmic Blazar Dragon".