In Cars (2006), the airplane contrails look like tire tracks.
During a fight scene in Fight Club (1999), you can see the narrator's head nod upward in the upper left corner, right as Tyler Durden is kicked in the face, subtly signaling their connection.
In "Hercules" (1997), Hades says "Guys, relax. It's only half-time" exactly at the 46-minute mark, the halfway point of the 92-minute movie.
In Up (2009), Carl wears a bow tie at the funeral because he never learned to tie a tie without Ellie.
In John Wick (2014), to get Daisy to wake John up, they had to smear bacon grease onto Keanu's face so the puppy would lick him.
In the final scene of WALL-E, Alaska no longer exists, a subtle and final nod to the film’s subplots on climate change.
In Deadpool (2016), the pizza place Wade orders From is called Feige’s Famous, which is possibly a nod towards Kevin Feige, president of Marvel Studios.
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The Twin Towers are still visible in one scene in the 2002 SpiderMan movie.
In Bryan Signer's X-Men films, (2000, 2003, and 2006) the X in Fox's logo is illuminated for a slightly longer time than the other letters.
40Willy Wonka and the Chocolate Factory
In Willy Wonka and the Chocolate Factory (1971), when reading the contract to Charlie and Grandpa Joe, Willy Wonka has to say “etc. etc.” in the middle of each sentence because he only has the left half of the contract.