In Yamada-kun and the Seven Witches, Yamada meets a duo of punk teens named Sid and Nancy, with Sid having a clear physical resemblance to Sid Vicious. It's also meant as a Sex Pistols reference in-universe, given that "Nancy" is just a nickname that the girl (whose real name is Haruko) adopted after meeting the guy (whose actual name really is Sid even though he's Japanese) and founding a music club with him.
In Harmonic Feedback, Naomi refers to Green Day as old-school punk, so Justin gives her a CD of punk music from the '70s and '80s that includes the Sex Pistols.
In Constantine, in order to prevent himself from hearing the noise that will be surrounding him, John listens to "Anarchy in the UK" on some earbuds to drown it out.
Logorama: When Ronald hides from the Michelin Man cop behind a wall, the Sex Pistols logo can be seen as graffiti art.
The Simpsons: In "Missionary: Impossible", Homer and Bart are watching Do Shut Up, a British sitcom about a family of Football Hooligans on PBS. The show opens with the father and son drinking from large steins while "No Feelings" plays.