How come no Star Trek fan has mentioned this one yet?
In the movie "X-men: Apocalypse", the 5000 year-old super-mutant-with-a-god-complex wakes up from his entombment in the 1980s Cairo.
Still disoriented he walks into Ororo´s home, in there he finds a TV set which is airing the "Star Trek" episode "Who Mourns for Adonais?", and then he learns in that episode that the "Age of Gods" is gone. and that pisses him. So Star Trek is to blame for his apocalyptical behaviour throughout the movie. :)
In the previous movie, "X-men Days of Future Past" there was also a Star Trek easter egg, as Hank McCoy was watching Star Trek in his workspace, the episode "The Naked Time" which also involves time travel.