In the Mystery Science Theater 3000 episode The Screaming Skull, the cast watch "Robot Rumpus" as a pre-movie short. Since Tom Servo and Crow are robots themselves, they identify more with the antagonistic robots than with Gumby or Pokey, and they're traumatized when the short ends with the robots dismantled.
A sketch from "Badunkadunk" has a teenage Incredible Hulk act as Gumby's stunt double.
A sketch from "Saving Private Gigli" has the Blockheads being put on trial for the murder of Gumby.
The Simpsons: The Couch Gag for "The Girl Who Slept Too Little" has the Simpson family roll into their living room as clay balls, and Gumby arrive a couple of seconds later. After a few seconds of rolling, the Simpsons form into themselves in claymation form, with Gumby doing the same.