Big Lipped Alligator Moment: The Flintstones part (where Homer sings the Flintstones theme as he's driving home from work) at the beginning of the episode. It has no place in the actual plot and it's never mentioned again. It's just there because it's funny.
Franchise Original Sin: This episode, considered one of the greatest of all time, is now the most fan-rewritten as a "modern" Simpsons episode to illustrate how badly the show has fallen into Seasonal Rot as it has a lot of elements that have come to be abused during its seasonally rotten years: celebrity cameos (Phil Hartman as Lyle Lanley and Leonard Nimoy as himself), the plot involving Homer having a new job that only lasts one episode, the Big Lipped Alligator Moment mentioned above, and the needless musical number that also has no plot relevance. Suffice it to say, these days, this would be more at home as a Family Guy episode, not a Simpsons one.
When Marge tells Homer that Sebastian Cobb is here to help stop the out-of-control monorail, Homer asks "Is it Batman?", Marge tells him "He's a scientist.", Homer tells her "Batman's a scientist...", making Marge say "It's not Batman!". Years later, the climax of Batman Begins has Batman trying to stop an out-of-control elevated train. Even more hilariously, he doesn't actually stop the train at all; he just thwarts Ra's al Ghul's plan, then lets the train crash.
The mutated squirrel and the appearance of the EPA become this when watching this episode after having seen The Simpsons Movie.
Moral Event Horizon: Lanley is clearly an amoral flimflam man from the get go, but the drawing that shows him gloating over the success of his plan really put him over the line. Failing that, the state of North Haverbrook post-monorail does a fine job of demonstrating how much of a snake Lanley is.