Issue #43 of The Simpsons has a story featuring pitches of spin-offs starring Poochie from The Itchy and Scratchy Show. One of them is "Poochie Babies", starring a baby Poochie alongside parodies of Piggy (Whiney Swiney), Fozzie (Spazzy Bear), Gonzo (Alonzo the Whatchamacallit), Scooter and Skeeter (Skidmark and Scurvy), Rowlf (Meowwlf), and Animal (Baby Bestial). They are watched over by a guy named Manny.
The Big Bang Theory: In the episode "The Justice League Recombination", after Zack and Penny bail on them, Sheldon says that he, Leonard, Howard and Raj no longer qualify as a Justice League and that they should switch to their Muppet Baby costumes.
Raj: I call Kermit!
Sheldon: I'M Kermit! YOU'RE Scooter!
Raj: Aw man, Scooter sucks! He's the Aquaman of the Muppet Babies.
Full House: In "Tough Love", Joey has a pajama-clad Baby Gonzo doll. When Danny replied that Nicky and Alex should learn to put away their toys, Joey says that it is his doll, and then he imitates the adult Gonzos voice, saying "The big guy sat on my nose" before squeezing Baby Gonzos nose and imitating a honking sound.
The Goldbergs: In "12 Tapes For a Penny", Adam becomes excited after finding out that this show is on.
An episode of Wonder Showzen features a sketch titled "Wonder Showzen Preemies" with the regular cast as babies in an obvious Muppet Babies spoof (Nanny even appears, shown from the socks up as a large pair of lips on legs in keeping with the style of Wonder Showzen, the preemies actually have "two nannies"). At the end of the sketch, the children watch their own favorite show, "Wonder Showzen Embryos."
Muppets Tonight: In "Episode 107: Sandra Bullock", Gonzo suggests putting on an episode of Muppet Babies (1984) to Clifford, carrying the Let's Build VHS release. This VHS gets tangled with a Seinfeld VHS that Zippity Zap is carrying, resulting in the creation of Seinfeld Babies, a show featuring Muppet infant versions of Jerry, Elaine, George, and Kramer.
AOK features a spoof of Muppet Babies called "Muppet Elderlies", which depicts the series' cast as seniors. In this spoof, Piggy breaks her hip and Bunsen and Beaker unsuccessfully attempt to perform surgery on her. Meanwhile, Fozzie gets on Kermit's nerves by making jokes about the situation.
Strong Bad Email: In "High School", several regular Homestar Runner characters appear as (in Strong Bad's words) "melon-headed babies with gigantic eyes and enormous imaginations". When the infant versions of Coach Z, Strong Bad, and Strong Sad imagine things, black-and-white photographic images appear behind their cartoon forms, referencing Muppet Babies' frequent use of old film footage. Homestar himself takes the role of Nanny, wearing red and white striped bloomers instead of green and white striped stockings.
American Dad!: In "Toy Whorey", plush toys of Baby Kermit, Baby Piggy, Baby Fozzie, Baby Gonzo, and Baby Animal are among the many toys in Steve's toy collection.
Bob's Burgers: In "Broadcast Wagstaff School News", Gene dresses up as Bob and imitates him throughout the episode. Near the end of the episode, when Gene decides to go back to being himself, Linda says, "I'll miss my Muppet Baby Bobby."
In "Little Orphan Hero", when Clara says having a suicide hotline sounds like fun, Foxxy reminds her of the time she adopted pit bulls and Foxxy had to find them a new home with the Muppet Babies. The scene cuts to two pitbulls viciously ripping apart Baby Kermit and Baby Gonzo. The DVD version of this episode features a slightly longer version of this clip, which also features Baby Fozzie already attacked and Baby Scooter being anal-raped by another pitbull.
"Drawn Together Babies" spoofs the series by telling the story of the Drawn Together characters as they were babies living together in a nursery. The opening theme is replaced with a direct spoof of the Muppet Babies' opening sequence, and portions of the episode cut to old black and white stock footage a la the live-action cutaways on Muppet Babies.
Garfield and Friends: In the U.S. Acres quickie following "Attack of the Mutant Guppies", after the Mutant Guppies scare off Orson and Wade, one of them suggests to the others, "Let's see if we can get a guest spot on Muppet Babies."
A sketch from "Schindler's Bucket List" features a murderer killing the adult versions of Gonzo and Fozzie. The murderer is later revealed to be Scooter, who wants revenge on the Muppets for drowning Skeeter in a kiddie pool (for beating up Fozzie and insulting Piggy) when they were kids.
A sketch from "Western Bay Hatch" features the Muppet Babies playing King Kong, with Kermit in the role of the titular ape. Gonzo and the other babies shoot Kermit down, and in reality, Baby Kermit is revealed to have died from falling off their "Empire State Building" made from a pile of chairs. Nanny then comes in and tells the babies to clean up the "crime scene".
South Park: In "Buddha Box", the PC babies are dressed like the 1984 versions of Kermit, Piggy, Gonzo, Fozzie, and Skeeter. However, the song and montage in the same episode spoofs the intro to the 2018 series.