Happy Feet: The scene in which the penguins dance for humans is a direct reference. The humans are even standing atop a hill that resembles Devil's Tower, while the penguins use dance to communicate like the humans communicated with aliens with music. The track on the soundtrack album is called "Communication".
Home (2015): The five-note vocalized intro to "Feel The Light" is reminiscent of the five-tone musical phrase used by the UFO.
Monsters vs. Aliens: The President tries to communicate with the alien robot by playing music — specifically, "Axel F".
Muppets from Space: After Gonzo's appearance on TV, Kermit encounters a bunch of people gathered around the Muppets' house. When he asks why they're there, a woman shows him a plate of mashed potatoes shaped like Gonzo and says they were drawn here by the alien.
Independence Day: After punching out an alien pilot, Steven Hiller quips, "Now that's what I call a close encounter."
Parodied in The Goodies episode "U-Friend Or Ufo", with the aliens kidnapping trombonists so they can communicate with the human race and landing their UFO directly on top of the Devil's Tower.
An episode of Adventures of Sonic the Hedgehog is entitled "Close Encounter of the Sonic Kind". In this episode, Sonic meets two aliens, Prince Charnock and Splorg, who have crash landed on Mobius. He befriends them and has to help them find the missing pieces of their spaceship before Charnock's coronation as king of the planet Rhombus, or else Charnock's baby brother will become king and destroy Mobius.
Big City Greens: In "Bill-eiver", Bill is convinced aliens are coming, and on one scene is sculpting something out of mashed potatoes.
Molly of Denali: A Freeze-Frame Bonus on Trini's laptop in "Cabbagezilla" shows a search result called Close Encounters of the Moose Kind.
Phineas and Ferb: In "When Worlds Collide", the silhouette of Candace against the light, seen when the planet arrives on their backyard, is a nod to this movie.
Rocko's Modern Life: In "Born to Spawn", Filburt's instincts are compelling him to head to his species' ancestral home of Kerplopitgoes Island. When Heffer prepares a tower of food covered in tahini sauce, Filburt goes insane and claws at it, carving it into the shape of Kerplopitgoes.
The Simpsons: In "The Springfield Files" after Homer repeatedly sees an "alien" and mails videotaped footage of this to the local news, Kent Brockman derisively calls it "Close Encounters of the Blurred Kind" and at a later festival in honor of the discovery, a school band plays the five-note piece from the film (plus one wrong note).
Also, in "Homie the Clown", after becoming subconsciously obsessed with the idea of attending Clown College, during dinner, Homer carves his mashed potatoes into the shape of a circus tent exactly as Roy carved Devil's Tower, complete with his tongue sticking out.
