In "Mad Money", one of the things Joey guys with his $5,000 savings bond is a 1964 Gumby and Pokey pinball machine, which was worth $1,275.
In "Aftershocks", Uncle Jesse finds Joey's Gumby figure in the garbage disposal.
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.
Gravity Falls: At the end of the "Clay Day" segment in "Little Gift Shop of Horrors", Soos inexplicably turns into an Expy of Gumby, even exclaiming Pokey's catchphrase "Holy Toledo!" when it happens and skating on one foot. However, Grunkle Stan and the twins, having had enough of stop-motion after having had to fight for their lives against evil stop-motion animated characters earlier that day, freak out and throw the Mystery Shack's TV at Soos.
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.