Dylan Dog referenced the film's deleted scene in a story featuring a murderous cartoon rabbit from the toon world. When Dylan enters the toon world, he gets involved in some sort of welcome party where he gets a toon dog head put over his actual face.
Fearless Leader: SHUT UP! THIS IS TOTALLY DIFFERENT!
Back to the Future Part II: In 2015, a Roger Rabbit doll is on display in a shop as part of their "Blast to the Past" sale. Appropriately, both films were directed by Robert Zemeckis and star Christopher Lloyd.
Pokémon Detective Pikachu is similar to Roger Rabbit in that it's a film noir set in a world where humans coexist with fantasy creatures, but more specifically it has a scene where a character is dangling from a skyscraper and a Pokémon hurts his fingers one by one, much like what happened between Eddie Valiant and Tweety Bird in Toontown.
In his Back to the Future Revisited review, The Nerd brings up the video game adaptation by Rare and LJN again, pointing out how the phone number Jessica Rabbit gives you now leads to an adult entertainment line, as well as showing how to win the final battle against Judge Doom.
In his review of Snoopy's Silly Sports Spectacular, while going through the game's backstory, the Nerd once again brings up the video game adaptation by Rare and LJN, as well as a Japanese Roger Rabbit game for the Famicom that became Bugs Bunny's Crazy Castlein its US release.
In his review of Super Mario Bros., Critic says that every time he hears Mario's accent (the same one Bob Hoskins did for Eddie), he expects Roger Rabbit to pop up.
In his review of the miniseries adaptation of The Tommyknockers, in response to a character humanizing to her collection of creepy-looking dolls, there is a brief sketch where Critic acts the same way with a bunch of Roger Rabbit dolls.
Animaniacs: In "Video Review", a VHS copy of film is on a shelf at the video store.
Benny the Cab appears as a guest in two episodes of House of Mouse; "Max's New Car" and "Mickey Vs. Shelby".
In the Muppet Babies (1984) episode, "Whose Tale Is It, Anyway?" Baby Bean Bunny goes missing and takes on the persona of a number of lagomorphic characters from various stories. When Janice captures something in a Box-and-Stick Trap, it's revealed to be Baby Rowlf playing the part of Eddie Valiant riding Benny the Cab. Bean overhears him looking for a tall rabbit in red overalls and funny cheeks, and responds to himself: "oh p-p-p-please," after Charles Fleischer's recognizable voice tick for Roger Rabbit. Later, in song, Bean appears as the character in an attempt to keep up with everyone's expectations.
In "The Looney Beginning", Buster answers Babs with "Roger, rabbit", to which she replies "You've got the wrong bunny."
In the short The Learning Principal (from the episode "Looniversity Daze"), Buster discovers that "The Great and All-Powerful Principal" is really Bugs Bunny operating a machine, to which Bugs replies "Eh, you were expecting maybe Roger Rabbit?"