Terrence Howard's line as James Rhodes foreshadowing the character's transition to War Machine consists of saying "Next time, baby" when considering suiting up with one of Tony Stark's armors. While Rhodes had his next time, Terrence Howard didn't, because he was replaced by Don Cheadle in Iron Man 2.
The jets chasing Iron Man are called "Whiplash One and Two." The villain in Iron Man 2? Whiplash.
Director Jon Favreau confirmed this was an intentional reference in an interview, though Whiplash was not intended to be the sequel's villain yet.
Director Kenneth Branagh is also a noted Shakespearean and has said he based some aspects of Thor on Henry IV. Fast forward a year later, when The Hollow Crown, an adaptation of three of Shakespeare's histories including Henry IV, comes out... and it's Loki playing Prince Hal.
During The Avengers, Cap and Tony got in an argument, where Cap kept telling Tony to put on the suit so they could go a few rounds. They finally got their long awaited match-up in this film. It turns out Cap can fight the suit on even ground, but gets overpowered once Tony analyzes and adapts to his fighting style.
When the above mentioned movie was released on theaters, wwwdotchargesdotcomdotbr character Tobby theorizes that the Green Goblin will be the Avengers' greatest foe. Spider-Man's debut in this film makes it more likely that Norman Osborn will appear in later movies.
In Boseman's first major role in 42, there's a scene where one of his teammates tries to console him amid a torrent of racist jeers from the fans by saying that they're a bunch of "crackpots still fighting the Civil War." Conversely, in an early Fantastic Four comic, the titular team is teaching Black Panther baseball. 50 years later, Boseman - the actor for Jackie Robinson - is now playing Black Panther!
There's a line of dialogue in Ant-Man where Spider-Man's powers are alluded to, but it was originally written as a throwaway gag and was not meant to foreshadow his inclusion in the MCU (since the Sony-Marvel deal didn't actually happen until after Ant-Man finished principal photography). Now it almost seems like a deliberate Brick Joke, considering that both Spider-Man and Ant-Man show up in the same movie for the first time.
The 2007 film Knocked Up has several characters reference Spider-Man 3 (which came out the same year), including the character played by Paul Rudd (the actor portraying Ant-Man).
While the film's logo originally presented "Captain America" in large letters above the "Civil War" tagline, changes made to the logo since then◊ have caused it to read more as if it says "Marvel Civil War", with "Captain America" as a visual afterthought. Guess what people have been calling the falling-out between Marvel CEO Ike Perlmutter and Marvel Studios President Kevin Feige, which is believed to have been incited by this movie?
Black Panther outrunning Captain America (to the point where Cap is forced to commandeer a vehicle) comes off as a sort of accidental Brick Joke, given the notorious "On your left!" scene in Winter Soldier.
The appearance of Spider-Man in the trailers came right after the announcement that J. K. Simmons, who played J. Jonah Jameson in the Spider-Man Trilogy, was joining the DC Extended Universe for the Justice League movie, this also makes more hilarious the memes where Jameson states he's leaving for Gotham since he's tired of waiting for pictures of Spider-Man.
In this film, Spider-Man is a young hero who latches on to Iron Man as a mentor. One of the phony trailers from Tropic Thunder has Robert Downey Jr.'s character playing a monk who has an affair with a novice, played by former Spider-Man Tobey Maguire, hailed even at the time as the closest we'd ever get to canon superhero slash fic.
In the comics, Tony Stark handed Peter Parker a copy of the Super Human Registration Act bill, which was still about to be discussed in Congress. He complained that it was as big as a Harry Potter book, and that he preferred to wait for the movie adaptation. Which he did: Spider-Man joins the MCU precisely when the movie adaption of the Act hit theaters.
The whole Empire Strikes Back gag got even funnier when Tom Holland revealed a year later that he'd actually never seen the original Star Wars trilogy.