"Funny Aneurysm" Moment: In one scene, when a character remarks that "[Being a security guard] is not that difficult," Mike riffs: "JFK Jr. could do it." This was intended to poke fun at the George magazine he founded, which was losing money and not taken very seriously as a publication. A little more than a year later, John F. Kennedy Jr. died in a private plane crash he himself was piloting (the crash was attributed to pilot error caused by his inexperience). Suddenly, this riff sounds a lot more mean-spirited than it was meant to be. (Hobgoblins originally aired: 6/27/98. JFK Jr's plane crash: 7/16/99)
And another one: a character picks up a gun, and Tom Servo riffs: "If found: please return to Hunter Thompson," a reference to Thompson's vast collection of firearms. About six and a half years later, Hunter Thompson committed suicide with a handgun.
Hilarious in Hindsight: Servo's riff on Daran Norris' emcee, "Proof that there's no life after drama club!" is ironic when you consider that Norris was one of two guys to have a career after acting in this stinkbomb. (The other was the guy who played Toe CheeseBack SweatSweat GlandButt Crack Road Rash, who you may remember as Zed's pal Maynard in Pulp Fiction)
Memetic Mutation: The "Hobgoblins" song sung by the cardboard duplicates is one, while Mike's "It's the 80s" song riff is used both straight and as a snowclone.
Mondegreen: Mike and the 'bots attempts to figure out the title of "Pig Sticker" "Pig Licker/Pig Liquor" "Kids Snickers" "Iced Chicken" "Swiss Knickers" "Lint Kicker" "Fish Picker" "Kiss Kicker"
Squick: The Ship Tease moment for Bobo and Pearl. Even in-universe the Bots are rightfully horrified.
The creepy David Lee Roth-esque woman that appears in Kyle's fantasy got this reaction.