- In "Meatballs or Consequences" the Warners, a trio of children, torture the Grim Reaper. A decade later, a cartoon came out with a similar premise about the Grim Reaper being tormented by some children.
- In "Hot, Bothered and Bedeviled", Ron Perlman voiced the Devil. Years later, he'd be Hellboy.
- "Hot, Bothered, and Bedeviled" began with a Saddam Hussein-esque dictator of Iraq getting dropped through a trap door into Hell. The Real Life version of this near the very end of 2006 would add a noose, but the principle's the same. Plus, 6 years later South Park: Bigger, Longer & Uncut would depict Saddam in a tumultuous romantic relationship with Satan himself.
- In "Critical Condition" the Siskel & Ebert parodies are tormented by Slappy for giving her a really bad review, finally being put inside an dinosaur movie and squashed. Cut to 1998, when Godzilla by Roland Emmerich comes out, and he just mocks them a little in-movie through Expies. Siskel even asked why he "didn't have the monster eat or squash them" after he went though the trouble of putting them in a monster movie.
- As an airline stewardess, Dot asks passengers if they want "Coffee, Tea, or Monster." These days, the joke goes from being a non sequitur to a pun, as there really is a drink out there called "Monster" (it's a brand of energy drink).
- In "One Flew Over The Cuckoo Clock", Slappy, driven crazy after too many talk shows, mentions that it's "Time for Montel and Phil on the Oprah Channel". Several years later, there really is an Oprah Channel! And Dr. Phil really does air on the network as well! (Though the Phil she was referring to was Phil Donahue, not Phil MacGraw)
- In a Star Trek: The Original Series spoof, Spork attempts a Vorkan Mind meld on Wakko, ending in Spork clutching his head, disoriented. He walks away, runs into Uhura and hits on her, saying "Helloo, Nurse!" Looks like J.J. Abrams was watching the show.
- The Mighty Morphin' Power Rangers parody episode "Super Strong Warner Siblings" had the siblings colors as red, blue, and yellow. Some later Power Rangers/Super Sentai seasons (and even some earlier Sentai ones that never made it to America) started with Power Trios that used the same colors. One of them was even a Self-Parody not too far off from "Super Strong Warner Siblings", titled Hikonin Sentai Akibaranger.
- In-joke for German SpongeBob SquarePants fans: In "The Party", Thaddeus Plotz (whose name in the dub is spelled with an a and umlaut, so it's really Thaddäus Plotz) is reading the invitation from the Warners, who suddenly pop up behind him without warning, and Plotz tells him not to do that. Yakko tells him to blame the writers, and we see Paul Rugg (voiced by Eberhard Prüter), laughing at the idea of the Warners being right behind him. In short, Thaddäus Plotz got screwed around by Thaddäus Tentakel.
- The reference that the Warners make to The Mask while hiding from their fans in "A Hard Day's Warners" gets even funnier when you remember that Yakko voices the title character in the animated series.
- In Hooray for North Hollywood 1, Mr. Plotz kicks George Lucas out for trying to get "another sequel to Star Wars". Considering what happened next with the prequel and sequel trilogies, it can get a nice chuckle in a different way now.
- "The Presidents Song" ended with then-current President Bill Clinton, but joked that his wife Hillary was the real power behind the throne by listing him as "the Clintons, Bill and Hillary" or "Clinton, first name Hillary". Since 2008, Hillary has run for president multiple times.
- In "10 Short Films About Wakko Warner", one of the short films features Wakko visiting the "Nanaland Retirement Home".
- Jess Harnell voicing Chandler in the Friends parody. Wakko's Japanese voice actor, Yu Mizushima, voiced Chandler.
- Another Friends one. Dot has a Running Gag where her name is really Princess Angelina Contessa Louisa Francesca Banana Fanna Bo Besca the Third. Season 10 of Friends would have Phoebe legally change her name to Princess Consuela Banana Hammock. But her friends can call her Valerie.
- In "Nothing But the Tooth", the Warners toss Rasputin the Mad Monk into a dentist's chair and announce that they need to give him some "Anastasia." A girl in a tiara and a poofy dress then hits Rasputin on the head with a hammer. Dot turns to the camera and deadpans, "Obscure joke. Talk to your parents." Don Bluth would bring the good duchess back into popular consciousness just a few years later.
- In "Jokahontas", there's a song called "Just The Same Old Heroine" which makes fun of how Disney movies using female heroines or princesses make the company a lot of money. Four years after the episode aired, Disney Consumer Products would make a merchandising program starring the three characters Dot becomes over the course of the song (Belle, Ariel and Jasmine), the titular character of Pocahontas (which they were spoofing) and Disney's other popular female heroines, Disney Princess, which was based on the popularity of princess movies among young girls.
- Speaking of Disney, one of the responses to Yakko's "It's that time again" during the Wheel of Morality was "to make fun of the Disney Channel?" This originally happened in 1993; at the time, it was meant to just be a light-hearted jab at Disney as Warner Bros usually did, with them being rival companies and all. Doubly so, because this was in the pre-Network Decay era when the Disney Channel still lived up to its name. It was still a premium subscription service, and they still focused on actual Disney programming such as classic shorts. In the modern day, with the channel now having undergone severe Network Decay and many of its shows hitting the Girl-Show Ghetto that have nothing at all to do with classic Disney animation, the light-hearted jab now feels like sincere satire that's even more appropriate than it was before.
- One of the Chicken Boo stories is a parody of The Karate Kid (1984) but has a title ("Kung Boo") that alludes to Kung Fu. Later on, the Karate Kid franchise had a reboot that retains the original title in spite of using Kung Fu instead of Karate.
- Continuing to speak of Chicken Boo, the short Katie Ka-Boo, which debuted Katie Kaboom, revealed that she and her family live in Pleasantville.
- In "Garage Sale of the Century", the man that Wakko turns upside-down with the garage door opener looks very much like Johnny Bravo.
- Tress MacNeille voices the Queen of Hearts in the show's Alice in Wonderland parody, "Mindy in Wonderland". Later, Tress would become the voice of Disney's version of the Queen of Hearts starting with the 1999 video game Disney's Villains' Revenge.
- In "Variety Speak", one of the titles on a movie theater sign was "Jurassic Park 5". In the later years, Jurassic Park would get four more sequels, with another coming in 2021.
- The credits for "Cutie and the Beast", which has the Warners complaining amongst themselves about the crew behind the show. One of the people they insult is the voice director ("The one who tells you to do the same line, like, 50 times?" "Yeah, and FASTER!" "Her?! I HATE HER!") note . Twenty-two years later, Rob Paulsen (Yakko) would become a voice director himself on Rise of the Teenage Mutant Ninja Turtles.
- Wakko's line: "A clown is my friend. A clown is not a big spider. A clown will not bite me and throw me in the basement," was an obvious allusion to It at the time, but it's become even funnier with the first season of the revival, which actually parodied the more recent film adaptation in one sketch.
- Expanding on that is Nickelwise, the parody of Pennywise, is voiced by Peter Stormare who was in Fargo...which Dot and Yakko parodied in "Hooray for North Hollywood, Part 2."
- In "Bumbie's Mom", when Slappy asks Skippy if she's ever lied to him before, Skippy says she has by saying that Magilla Gorilla is a woman. Although Magilla may still be male, several other male Hanna-Barbera characters would receive Gender Flips in Jellystone!.
Hilarious In Hindsight / Animaniacs