Iron-Man 2 (2010) - Black Widow's alias Natalie Rushman's resume includes experience at Hammer Industries, which is perhaps why (later in the film) she is already familiar with the security, building layout and computer systems at Hammer Industries.
In Captain Marvel (2019), Vers picks up the movie The Right Stuff (1983) inside the Blockbuster Video. The Right Stuff takes place at Edwards Air Force Base, which is where she was stationed while in the Air Force.
In Spider-Man: Homecoming, at the start of the scene where ‘MJ’ is revealed to the audience, a kid dressed as a tiger is seen running right through the middle of the frame. For fans of the comics, this is a lovely little piece of foreshadowing because MJ’s nickname for Pete is ‘Tiger’.
In Captain America: Civil War, part of Sharon Carter's speech from Peggy's, "Plant yourself like a tree" bit was taken directly from The Amazing Spiderman #537 when Captain America tells the same thing to Spider-Man.
In Thor: The Dark World (2013), Natalie Portman couldn't make it reshoot the final kiss scene. When asked to choose from a lineup of women to take her place. Chris Hemsworth instead brought in his wife, who wore Natalie's clothes and wig to shoot the final kiss.