Jerry Maguire: After Jerry signs Cush back (or so he thinks), while driving to the airport, he looks for a song on the radio to sing along to in order to express his joy. The Rolling Stones' "Bitch" comes on first, which doesn't fit, and he switches to "Angel of the Morning" by Merrilee Rush (too high), and then "She" by Gram Parsons (which he doesn't know), before finally landing on "Free-Fallin'", which he does sing along to enthusiastically.
Jonathan Demme has used Petty's music a couple of times:
In The Silence of the Lambs, Catherine sings along to "American Girl" on the radio shortly before she's kidnapped.
In Ricki and the Flash, "American Girl" is the first song we hear Ricki and her band play.
In Marriage Story, Nora says "Wasn't it Tom Petty who said the waiting is the hardest part? I represented his wife in their divorce, I got her half of that song."
In Like No Other Boy, Chris, Cheryl, and Tommy listen to Tom Petty on the radio as they drive to the Weller Institute. Cheryl's favorite song is "I Won't Back Down."
Star Trek: The Next Generation: In "Phantasms", Data's nightmare where he imagines Counselor Troi as a cellular peptide cake (with mint frosting!) and takes a slice is similar to the video for "Don't Come Around Here No More".
In "The Cartridge Family", Homer decides to purchase a gun, but the gun shop owner tells him there's a five-day waiting period while they run a background check on him. After he dejectedly heads home, he sits on his lawn and asks himself "How am I supposed to last five days without shooting something?". He spends the next five days sitting on his lawn, seeing different people and things he'd like very much to shoot with a gun: Flanders (twice), Patty and Selma, a row of ducks, rabbits, and a truck owned by Target (because of the famous bullseye logo on the side), while "The Waiting" plays.
Tom appears As Himself in "How I Spent My Strummer Vacation" as the lyrics workshop teacher at Mick Jagger and Keith Richards' Rock'N'Roll Fantasy Camp.
Tom Petty: (strumming acoustic guitar) Lyrics are the hardest part of songwriting, but when you come up with something meaningful and heartfelt...