Accidentally Accurate: Interestingly, the card effect and artwork position of Stoic of Prophecy perhaps unintentionally matches the meaning of the Hanged Man in another way. The Hanged Man in the tarot card is upside down (as cards often are in the anime when characters discard) then the card means what it normally does: sacrifice and selflessness. When the figure in the card is upright (as it would be if summoned) it means an inability to act, which is reflected by this card being weak when on the field.
Adaptation First: The dubbed anime came out in the west before the manga did, so it's more well-known than the English manga. Sad, but true. In America, people are probably more familiar with the dubbed and subbed anime than they are with the manga (as a whole). This is true with most shounen anime. But within the American Yu-Gi-Oh! fandom, there are probably more anime fans than manga fans.
Heck, there are probably even more fans of the card game than there are of the manga. Even Toei's anime series is more talked about than the manga, possibly because of The Abridged Series.
Bad Export for You: The European releases of the first few Booster Packs were missing several cards. Fortunately, these were restored in later releases.
Many of the more recent Structure Decks are like this, either being edited to remove high-rarity cards, or in two cases scrapping the deck altogether and importing the new cards in them as add-ons to normal sets.
The TCG missed out on the chance to get Dark Magician Girl as drawn by Kazuki Takahashi in the 10th anniversary pack. Justified, however, because Takahashi refused to bow to Executive Meddling to have Dark Magician Girl censored.
The localized version of Yu-Gi-Oh! ZEXAL World Duel Carnival was severely watered down from it's Japanese version. 28 playable characters, a database mode, duel profiles, ending pictures, device mode, ending pictures and se;ectable music have been removed, seemingly for no reason.
Masked HEROs and Vision HEROs, formerly manga-only cards, have finally started appearing as alternative support cards to Elemental HEROs.
Also applies to a few other Yu-Gi-Oh! games from the manga, particularly Dungeon Dice Monsters and Capsule Monster Chess. Unfortunately, they failed to be as popular as the OCG and eventually died on the wayside, quietly. Although they were turned into video games which did decently.
Executive Meddling: Kazuki Takahashi's editor told him to hurry it up during the Millennium World arc because of the declining reader interest due to the long Battle City arc. Needless to say, a lot of plot threads that were originally intended to be expanded upon didn't see the light of day, especially since Kazuki Takahashi fell ill during it all.
David Willis voices both Gozaburo Kaiba and the nameless Rare Hunter in the English dub. Coincidentally, both characters use an Exodia deck (though different versions) and both suffer from the weakness of thinking that having Exodia (or Exodia Necross in Gozaburo's case) is all they need to win.
Keep Circulating the Tapes: Because of legal issues surrounding Shunsuke Kazama's (the voice actor of Yugi/Dark Yugi) contract note Shunsuke Kazama is a trainee Idol Singer managed by Johnny's Entertainment, who is notorious for its tight regulation of its acts, it's impossible outside Japan to find any official release of the anime other than the edited dub version. 4Kids attempted to release unedited DVDs of the show, and later put subtitled episodes directly on YouTube, but both of these releases were cancelled, leaving people who don't want to endure 4Kids' edits out of luck if they want to be legitimate customers.
LittleKuriboh has noted that he doesn't abridge "Season 0" because good quality, unsubtitled episodes, are nearly impossible to find, but of course they have to exist somewhere out there because new fansubs of it keep popping up.
In the Card Game, there are some cards that just can't be bought normally, first hand as in the way they were meant to be; the most famous example is the first edition of the 3 Egyptian God Cards: foiled, shiny and Colour-Coded for Your Convenience, these were packed with the GBA game Yu-Gi-Oh! Reshef Of Destruction; people went crazy for this game just to get the cards, a great deal of the copies sold for this game was due fans wanting the cards, eventually retailers came to know that some people just bought the game for these cards, so they would gladly put a reminder for used copies Does Not Contain The Limited Edition Cards!, people on eBay followed suit as gullible fans also thought that buying a $20 copy of the game would grant them shiny and exclusive cards that were sold for about $100 separately.
Name's the Same: The name Paradox has been used at least three times; the Labyrinth brothers Para and Dox, the Grandpa lookalike in the Reshef of Destruction game, and the antagonist of the Bonds Beyond Time movie.
Fire King Avatar Yaksha is the second card that is a reference to Yaksha; the first is "Yaksha". Interestingly, these two cards have the opposite Attribute ("Fire King Beast Yaksha" is FIRE; "Yaksha" is WATER).
"Gimmick Puppet Gear Changer"'s name is similar to "Gear Changer". Also, both cards' are gears with effect that involves changing Levels.
Hieratic Dragon of Nebtet comes from the Egyptian God, Nephthys; that name is shared with "Sacred Phoenix of Nephthys" and "Dark Nephthys".
Ryko is spelled that way to avoid any association with Raikou, a legendary Pokémon.
The Blue-Eyes Shining Dragon was released as a promo for the movie in 2004. The card required to Summon it, the Blue-Eyes Ultimate Dragon, wasn't released until over a year-and-a-half later. Though both were available in Japanese, OCG cards are not allowed when playing the TCG.
Recent TCG sets have included more cards than the corresponding OCG set- some of these are cards that were previously OCG only, while others are cards that are exclusive to the TCG. In turn, TCG only cards have recently begun to be released in the OCG through the Extra Pack sets. Eventually the two card pools may become equal...
Sometimes this applies to the video games as well. Tag Force 6, hotly anticipated by some as the first video game to feature Xyz cards, was not released outside of Japan.
Word of God: Two, as a matter of fact; until 2008, card rulings were given by both Konami and UDE, and they didn't always agree with each other. Many cards actually have different rulings for the TCG and OCG versions of the game because of this.
It's notable that in case of disagreement between the companies, it's rare but not impossible for the TCG's claims to gain worldwide sway in terms of deciding how cards actually work once word of the disagreement gets across the Pacific - and any cases where the TCG's claim does stand ultimately stand because the OCG and TCG management departments agree that "that works better for our purposes." Ultimately, the game's management (at least in some senses, including rulings) considers YGO to be 1 worldwide game with different names in different regions; and the OCG is the origin point, thus it's the locale that holds sway a good chunk of the time. Points of disagreement that aren't ironed out are simply points of disagreement that either went unnoticed or were noticed but deemed unimportant; but while a disagreement DOES exist, you are required to follow the orders of your own jurisdiction, regardless of whichever side you think will "win" the argument.