Golden Wind has Pesci, whose Stand is a fishing rod named Beach Boy, with a hook and line that can pass through solid objects and detect body movement.
Steel Ball Run has Sloop John B and his race horse, Catch a Wave, who are both named after songs by The Beach Boys.
JoJolion has Ojiro Sasame's Stand, Fun Fun Fun, which can control a person with an open wound by hovering above them.
The JOJOLands has Barbara Ann Joestar, named after the "Barbara Ann" song.
In Roger & Me , laid off GM plant worker Ben Hamper discussed how he embraced "Wouldn't It Be Nice" when he had a nervous breakdown upon losing his job that ultimately landed him in a mental hospital. The film then uses the song to contrast the economic problems of Flint, Michigan at the time.
Good Morning, Vietnam: When the radio personnel are debating what entertainment to get to play for the troops, Adrian Cronauer tells his boss to book the Beach Boys, while Dreiwitz, one of the other DJs, jokes the band is too busy playing at the beach.
If I Fall, If I Die: When Diane first met Arthur, he had a wholesomeness that reminded her of the Beach Boys.
Juniper Sawfeather: In Whisper of the Woods, June and Carter listen to "California Girls" on the radio. Carter tells her, "It's your song! For when you go to San Diego and get a job at Sea World!"
The Big Bang Theory: In "The Earworm Reverberation", Sheldon is obsessed with a song stuck in his head that he can't name. He eventually identifies it as "Darlin'" by The Beach Boys.
Penny: Do you even like the Beach Boys? Sheldon: They have "beach" right in the name. What do you think?
The Goldbergs: In "George! George Glass!", Barry wants to go to Live Aid but can't get tickets. Bev offers to take him to a Beach Boys concert she's going to, but he dismisses the offer... neither of them realizing that she was going to see them perform at Live Aid.
The Muppets Mayhem: Episode four features a cover of “God Only Knows” performed by the Electric Mayhem.
Bioshock Infinite features a barbershop quartet cover of the song “God Only Knows”.
EarthBound samples the Lyrical Cold Open of "Deidre" for the Cave of the Past's BGM. As the sample is reused for the track "Amalgam" in Undertale, the "Deidre" reference carries over there as well.