1.During the time travel sequence in Avengers: Endgame, Thor mentions that they're going to lunch. This is a reference to the famous shawarma post-credits scene.
2.In Avengers: Infinity War, Tony and Pepper talk about getting married on August 27th, which is Robert Downey Jr.'s real-life wedding anniversary.
3.In Spider-Man: Homecoming, there's a sign on the freeway on the way to Washington, D.C. that references cleanup for the major crashes in Captain America: The Winter Soldier at S.H.I.E.L.D. headquarters.
4.In Avengers: Endgame, there's a pair of ballet pointe shoes in Natasha's office. This is a nod to her backstory in the comics, where she was given fake memories of being a ballerina...and also possibly a hint at hobbies Nat took up after the Snap to keep her spirits up.
5.When Thor is about to give his spiel about the Reality Stone, he puts in some eyedrops. But he only does it in one eye, because his other eye is mechanical.
6.In Avengers: Endgame, Tony gets the idea that solves the time travel problem when he sees a photo of him and Peter Parker holding a diploma upside-down.
7.In Ant-Man and the Wasp, Hope mocks Scott for referring to Captain America as "Cap." In Endgame, Scott gives her a look after she does the same thing.
8.At the beginning of Avengers: Endgame, right after the Snap happens, the sound of wildlife (i.e. birds chirping) becomes suddenly much quieter.
9.In Guardians of the Galaxy, Gamora is mentioned to be the last survivor of her people, indicating that Thanos's "balancing" plan failed horribly on her planet.
10.In the same sequence in Guardians of the Galaxy, Quill is mentioned to have a translator implant, which explains why he can communicate with a number of different alien species.
11.Whenever Thanos uses the Infinity Gauntlet, you can see the corresponding Infinity Stones that he's currently using light up. Here, he uses the Soul Stone to figure out which projection of Doctor Strange is the real one, then uses the Power Stone to break the illusion.
12.Similarly, you can see some green light around Thanos's wound right before he steps into the portal and escapes Wakanda. This suggests that he used the Time Stone to heal up the wound.
13.After the events of Thor: The Dark World, when Thor believes Loki is dead, he adds a lock of Loki's hair to his braid.
14.Ego's car at the start of Guardians of the Galaxy, Vol. 2 has the same color as Quill's ship.
15.In Spider-Man: Homecoming, Michelle is reading Of Human Bondage, which is about an orphan who goes to live with his aunt and uncle, just like Peter did.
16.Also in Homecoming, Bruce Banner is pictured on a wall of famous scientists in Peter's physics classroom, including Nikola Tesla, Marie Curie, and Isaac Newton.
17.Next to the Thai restaurant where the Parkers eat in Homecoming, there's a sign for the "Korean Church of Asgard," indicating that people started worshipping the Norse gods again after Thor's arrival on Earth.
18.When Doctor Strange uses Thor's hair to find Odin at the start of Thor: Ragnarok, he creates a triquetra or "infinity knot" symbol, which appeared when Odin enchanted Mjolnir.
19.Steve removes his Avengers patch and eventually the star and color from his outfit after he stops being Captain America.
20.In Iron Man 2, a screen shows an "incident at Culver University," referencing the battle between Hulk and the military in The Incredible Hulk (2008).
21.In Age of Ultron, Clint shows off his newborn son to Natasha over Skype. The onesie shows that Clint gave the baby the middle name "Pietro," after Pietro Maximoff aka Quicksilver, who saved Clint's life during the battle against Ultron.
22.When Thanos's ship attacks the Avengers compound in Endgame, Scott instinctively shrinks in order to survive the blast.
23.And finally, in Endgame, Tony and Steve both prove each other wrong referring to the insults they threw at each other in the original Avengers movie.