Casper's Haunted Christmas: When Casper is grilled for not meeting his scare quota, it's mentioned that he spent last Halloween at home watching Free Willy 3.
Cats Don't Dance: The film ends with a montage of parodic movie posters featuring the main cast, including Tilly and Pudge on one for Free Tilly.
In John Pinette's "I'm Starvin'!" routine, he recounts his disastrous visit to a water park. Due to the construction of a certain slide combined with a quirk of fluid dynamics, he got launched into the parking lot, over the head of a family of foreign tourists who had just seen the movie. They were extatic, and insisted on taking a photo of him when he got back in.
The Angry Video Game Nerd: In Part One of his review of Sonic the Hedgehog (2006), the Nerd finds out that the goal of the first stage, Wave Ocean, is to close a gate to prevent a killer whale from escaping. He then says that he expected the goal to be to set the whale free, like in Free Willy. After that, he shows the poster for Free Willy and asks the viewers if they think it looks like Jesse is punching Willy, then asks who would be able to punch a whale so hard that it becomes airbone.
In "The Boy Who Knew Too Much", juror Homer tries to deadlock the Quimby trial so he can sequester at a fancy hotel that comes with free room, free food, free swimming pool, free HBO and Free Willy. Later, Homer watches a "director's cut" of the film where Willy fails to make his big jump and crushes Jesse.
Annie: Oh, no. Willy didn't make it. And he crushed our boy! Glen: Ew. What a mess. Homer: Ohh, I don't like this new director's cut!
In "Treehouse of Horror XI", the segment Day of the Dolphin has parodic scene where Lisa helps Snorky the dolphin escape the aquarium. Snorky makes the jump, but he hits Lisa with his tail in the process.
In "Chef's Chocolate Salty Balls", a film producer remarks that a movie about Mr. Hankey could be "the next Free Willy".
The episode "Free Willzyx" is a brutal parody where the boys are tricked into sending a seemingly talking orca to the Moon.
Tiny Toon Adventures Spring Break Special: As a killer whale is freed, it jumps over a gate and lands on Elmyra, with Babs singing "Will U B Hare", a parody of Michael Jackson's "Will You Be There".
