Probably the most high-profile (that references something outside of M:tG itself anyway) is Nevinyrral's Disk. "Nevinyrral" is "Larry Niven" spelled backwards. Niven wrote a series of stories about magic as an exhaustible resource, the nature of which was proven in the story "The Magic Goes Away" by a wizard who enchanted a spinning disk in such a manner that it used up all the mana in its vicinity, exploding violently in the process.)
Likewise, the flavor text for the Starter 1999 version of Goblin Mountaineer is one word off from the second phrase of the theme song to The Beverly Hillbillies. "Goblin mountaineer, barely keeps his family fed."
The flavor text of Deicide (a term that refers to killing a god, but which outside of the genre of fantasy is usually used in a religious sense to refer to the death of Christ) references Jesus' last words in John 19:30.
The Star Wars Customizable Card Game is made of this trope: Smuggler's Blues obviously, but also Mostly Armless and Bionic Hand "We can make him better, stronger, faster."
Yu-Gi-Oh! is absolutely loaded with Shout Outs to Konami games, mostly notably the Gradius archetype: so far, a card exists for the original ship, an upgraded version of same, the second player ship, the ships from Gradius Gaiden, most of the various ship bosses (complete with support card Boss Rush), the game's power-ups, at least three of the other various bosses, and at least five of the game's enemies. Plus, they synergize pretty well with the cards based on the protagonist ships in Xexex and Thunder Cross. And let's not even get into the set of Union Monsters based on Aitsu, Koitsu, Soitsu, and Doitsu...