When driving to Hollywood, Kermit and Fozzie encounter Big Bird, who is walking to New York City with dreams of breaking into public television. Later in the film, a picture of Big Bird can be seen in the Electric Mayhem Bus, along with a photo of the Sesame Street Muppets from 1972.
Kermit and the gang audition for Lew Lord, a homage to Lord Lew Grade, the producer and mogul who enabled Jim Henson to produce The Muppet Show.
As the Muppet gang is walking down the street, shortly before discovering Pete's Luncheonette, a street vendor can be seen in the background, selling hand puppets to passersby.
Although part of the gag reel, there is a scene where Gonzo and Rizzo are sitting on the shelf with the busts. Rizzo takes one look at the bust of Shakespeare and exclaims, "Hey! It's Frank Oz!". Gonzo adds, "They coated him with plaster! Frank, speak to us!"
According to the book Muppets from Space: The Making of Muppet Movie Magic, the "door in a jar" provided by Muppet Labs was intended to be a replica of the front door of 123 Sesame Street. As realized, there are several differences. 123 Sesame Street's stoop has 6 steps and the "door in a jar" had 7, and the window above the door differs from the Sesame design. The "door in a jar" was also red whereas 123 Sesame Street's door was green (the door of 123 Sesame was red for a period of time but that did not happen until 3 years after Muppets from Space was released). However, the door is a replica of the door used in The Adventures of Elmo in Grouchland, which was filmed concurrently with Muppets from Space.
The newspaper that Kermit reads during the breakfast scene is called the "Hensonville News Observer".
There are several behind-the-scenes references in the pet store. Performer and crew names include Frank and Steve's Monkey Shines, Goelz Guppy Grub, Nelson's Super Fine Cat Food, Sir Richard's Hunting Dogs, and Lazer Pet Academy. Products include Salmon Friends fish food and Puppet Chow.
The vehicle that Mary and Carlos work on in her classroom is the same one the gang gets from Mad Man Mooney's.
"The Standard Rich and Famous Contract" Kermit signed in The Muppet Movie is featured.
Mad Man Mooney's makes a re-appearance, now renamed "Mad Man Mooney's and Son." Sweetums is shown working there again and is forced to chase after the gang's car again.
Clips from The Muppet Show are used during Walter's origin story at the film's beginning. Later, short audio clips are used when Kermit first enters the dilapidated Muppet Theater.
When Tex Richman reads in a magazine that the Muppets have gotten together again, Uncle Deadly and Bobo begin to sing "Together Again." Later, Walter plays a few bars from it on a backstage piano.
The Muppet Theatre's curtain rail system is branded with its installation date - September 24, 1936, Jim Henson's birthday.
The cake topper on Walter's birthday cake is a repainted Kermit figurine.
Walter's bedroom is filled with Muppet collectibles and memorabilia, including a Muppet Babies lunchbox.
After the question is raised of Walter leaving the Muppets after a whole film was made about him joining them, Rizzo and Robin point out that it was made at the expense of other well-known characters being left out, referencing their reduced roles in the previous film.
Referencing dialogue in The Muppet Movie, Kermit and Fozzie give each other directions when coordinating their escape with their feet through the bottom of Le Maximum, "Bear, left." "Right, frog."