Contest Winner Cameo: Quite a few cards are designed by fans and they appear for a few episodes. Performapal Trump Witch appears to be the only lucky card that appears regularly.
Defictionalization: Long before its official release in the card game, there was another version of the Seal of Oricalchos but there were only 15 in the entire world, used in a single special tournament by Upper Deck employees where players could duel them. And yes, their version was just as overpowered as it was in the show, which is why the legal version got nerfed.
Truth in Television: Remember Pegasus, the guy who had those overpowered Toon cards that were never released into circulation due to being too strong?
Fan Nickname: Chaos Sorcerer was nicknamed "the poor man's Chaos" due to its Common rarity, as opposed being Secret Rare like the Envoys.
Fountain of Expies: The particular style of outfit Dark Magician wears has inspired an entire archtype of Magician cards, and of course he has many evolved forms.
In a roundabout way, it's now tradition for the protagonist's key monster to have 2500 Attack, while to parallel the Blue-Eyes, their rival's key monster has 3000 Attack.
Dark Magician Girl. Let's see: Magician's Valkyria, Gagaga Girl, Performapal Trump Witch, and Card Ejector.
The mighty Blue-Eyes White Dragon: Cyber Dragon, White Night Dragon, Red Dragon Archfiend, and especially Galaxy-Eyes Photon Dragon, most of which are played by major rivals and have equivalent attack and/or triple-fusion or Xyz variants. See below.
And for Blue-Eyes Ultimate Dragon, we have Cyber End Dragon, and Neo Galaxy-Eyes Photon Dragon. (Though the latter differs in that it is a triple Level 8 material Xyz monster.)
One can think of Red Nova Dragon as a Expy to BEUD as well considering that just to summon Red Nova takes two Tuners, meaning he usually has 4500 or more attack.
Franchise Killer: Allure Queen and Dark Lucius are believed to be the cards that finally murdered the LV archetype - Allure Queen for being too underwhelming in even its LV7 form, Dark Lucius for having its LV8 form be the only worthwhile form, and both for completely losing their effects if not Summoned using their lowest form, making Summoning either a slow (and often Unwinnable) grind.
No Export for You: The Anniversary Pack artwork for Dark Magician Girl was not included in the TCG release. According to most sources, this is because Kazuki Takahashi refused to edit the art for release outside Japan.
Prior to the official release of Primal Origin, there were sources depicting Starduston as a fake Duston version of Stardust Dragon. It also had a effect highly reminiscent of Stardust Dragon: During either player's turn, when a card or effect is activated that would destroy a card(s) on the field: You can Tribute this card; negate the activation, and if you do, destroy it. You can only control 1 face-up Starduston.
Konami got Kazuki Takahashi to do some artwork for several of the most iconic cards in the game. This included a very well drawn Dark Magician Girl card. However, when they requested that he make some changes to his art for an American release(specifically, toning down her cleavage), he refused. As such, there was no American release for that card.
According to the Duel Art artbook by Kazuki Takahashi, Magi Magi ☆ Magician Gal was originally intended to be simply another "Dark Magician Girl" art to act as a female counterpart to the anniversary art of "Dark Magician." It was later made into a new Xyz monster.