"The cheese stands alone" is a line from a song. The song is called "The Farmer in the Dell." I don't remember all of the words, but it's not a deep or meaningful song.
Because people thing "random" means funny, a lot of random things were thrown into the set, Unglued. And when people try to come up with random things, for some reason they always wind up picking foodstuffs. There is probably some psychological explanation for this.
In Unglued, they also liked picking stuff that had to do with cows and chickens. And they liked picking stuff out of well-known songs. Cheese is a foodstuff, a dairy product, and "the cheese stands alone" is a line from a well-known song. It was PERFECT for Unglued.
And, as you might notice, the card makes no further references to "The Farmer in the Dell." The flavor text is a joke about the title of the card itself.
I used to fetch it with Ring of Ma'Ruf in highlander games, then cast it and play Kaervek's Spite while it was on the stack. Good times...
