Shadow in the Cloud: British Flight Officer Maude Garrett sees a gremlin tearing the plane apart and can't convince the rest of the crew it exists at first, until the gremlin starts attacking them directly.
Animaniacs: In "Gimme a Break", Slappy tries to get away, but ends up seated next to a Shatner caricature, who says, "There... is... someTHING... on... the PLANE!" When Slappy moves away from Shatner, he picks up a device and says, "Beam Me Up, Scotty!."
Futurama: The Scary Door episode seen at the beginning of "I Dated a Robot" has parodies of several Twilight Zone episodes, including "Nightmare at 20,000 Feet". Also, in "Zapp Dingbat", Zapp Brannigan, who is a Shatner Expy, is bored and asks Kif to go outside the ship and pretend to be a gremlin.
Johnny Bravo: In an episode where all three segments parody The Twilight Zone, the first segment parodies "Nightmare at 20,000 Feet", with a clown replacing the gremlin.
The Simpsons: The second segment of "Treehouse of Horror IV" is called "Terror at 5 1/2 Feet" with Bart in the Shatner role and the school bus replacing the plane. At one point, the bus bumps off Hans Moleman who is driving an AMC Gremlin.
The Tiny Toon Adventures Halloween special "Night Ghoullery" parodies this episode with Plucky imitating Shatner's staccato delivery, and references to Shatner's role on Star Trek by having Uhura appear as a flight attendant. The gremlin in this case is portrayed by the gremlin from Falling Hare.