The card Persecute Artist doesn't let the caster choose Rebecca Guay. This is a nod to the time when rumors that Guay was being fired as a Magic card artist led to an Internet Backdraft.
The twelfth edition's print of Giant Spider states that "The wild is always changing, but it does have a few constants." This is probably a reference to the fact that by this point, Giant Spider was the only card (aside from the five basic lands) that has been in all core sets since the game's beginning.
Lightning Bolt was cut from the main set after Fourth Edition as too powerful and replaced by cards with basically the same effect but less powerful/mana efficient. It was reintroduced in the 2010 set with the flavor text, "The sparkmage shrieked, calling on the rage of the storms of his youth. To his surprise, the sky responded with a fierce energy he'd never thought to see again."
A few cards in the Yu-Gi-Oh! card game are based upon storylines from the original manga from before the card game came to prominence:
Zombyra the Dark is based upon a character from a Show Within a Show Zombire, who is a Spawn Expy. Like Spawn, he gets closer to death the more he fights, represented by an ATK reduction.
Dark Master - Zorc was the Big Bad of the Monster World story arc, which was a Table Top Game. From that comes the die-rolling effect, including the fact that a lower roll is better and the highest roll is a fumble. And the art for its corresponding ritual spell card, Contract with the Dark Master, is based on the scene in which Zorc first reveals himself by transforming from a seemingly friendly NPC.