- The opening sequence references the ultimate fate of Sunnydale in Buffy the Vampire Slayer with the misfiring portal flare, collapse wave and fleeing vehicle.
- After Loki escapes and hypnotizes a couple of agents and the team is meeting up, Fury wonders how Loki used the cube to turn two of his agents into "flying monkeys".Thor: Monkeys? I do not understand.
Captain America: I do! I understood that reference.
- Iron Man throwing a nuclear missile into outer space is a big hello to Superman.
- Loki is brought to "face Asgardian justice" in chains and a face mask resembling that of Hannibal Lecter. Anthony Hopkins plays Odin in Thor.
- Tony wears a Black Sabbath shirt from their "Never Say Die!" era; one of Black Sabbath's hits is "Iron Man".
- When Thor and Loki are talking on the mountaintop, a couple of ravens are seen flying by.
- Tony's "reverse the polarity" references many sci-fi shows.
- Tony calls Hawkeye "Legolas", Thor "Point Break", and Loki "Reindeer Games" and "Rock of Ages".
- Loki taunts Nick Fury about coming so close to unlimited power, the very same phrase used by Palpatine when he killed Mace Windu in Star Wars. Both recipients of the speech were played by Samuel L. Jackson.
- Tony briefly asks JARVIS if he's ever heard of the story of Jonah, immediately before he goes through the mouth of one of the leviathans and blows it up from the inside out.
- The shot during the final battle when Cap, Black Widow and Hawkeye are looking up at the portal watching the first Leviathan come out is shot in the exact same manner in which Peter, Ray, and Egon look at Gozer's portal opening in Ghostbusters (The scene is at 2:19.)
- Iron Man's pose during his entrance in Germany: Insane Amounts of bonus points for the circumstances: Captain America is on the ropes and now on the ground without his shield against Loki in both instances, and Hawkeye is using Loki's monologue to his advantage.
- Iron Man and Captain America have to work on their ship's engines in flight, with Stark telling Steve to open an access panel. Steve finds himself faced with a mindboggling array of electronics, much as Jayne did while helping Kaylee in the original pilot of Firefly.
- Captain America punching the punching bag so hard that it breaks and effortlessly hanging up a new one is taken from a scene in Buffy the Vampire Slayer, switching Buffy for Steve.
- Cap and Iron Man perform a tag-team move from Marvel Ultimate Alliance 2 in the penultimate battle.
- That same scene is equally reminiscent of Kingdom Come. Especially considering the nuke was fired by the UN (or similar substitute) with the knowledge it would wipe out the known superhero population. They even have a red-and-gold costumed hero making the sacrifice play to take the nuke out of range, though in this case, Tony survives.
- The moment where Thor's lightning supercharges Iron Man's armor. The same thing happened during their first battle in the comics and in The Avengers: Earth's Mightiest Heroes!.
- Tony Stark wanting shawarma, and the team going out to get it in The Stinger, is a shout-out to Buffy the Vampire Slayer; one of Whedon's favorite memories from the show was Nick Brendon's audition, after which he asked if anyone wanted to go get shawarma.
- Enver Gjokaj appears in a brief scene as an NYPD officer named Saunders.
- One happens in the Gag Reel where Downey asks if they're gonna have a gag reel, "...like Smokey and the Bandit?" The beginning of the gag reel is set to "East Bound and Down" by Jerry Reed; the main theme from said film.
- In the interrogation scene introducing Black Widow, Johannsson's character's red hair and costume are a shout-out to Moira Shearer's character in The Red Shoes (1948). The Russian general also says "We don't need Lermontov to deliver the tanks". Lermontov is the name of Shearer's co-star's character.
- One of the more tense moments is an extended, one-on-one fight between Thor and an out of control Hulk. The two of them also met in The Incredible Hulk Returns (although in that one Thor is enjoying the fight rather than trying to get Banner to calm down.)
- During Steve and Tony's conversation about Loki. Captain America said that Loki packs a mighty wallop Bonus points since Tom Hiddleston voices James Hook and portrayed Loki and both of the movies are produced by Disney.
Steve Rogers: (refers to Loki) I don't remember it being ever that easy. This guy packs a wallop.
- From the Avengers:
James Hook: Cause the blue fairy dust surely packs a mighty wallop.
- From the Fairies Franchise song: A Frigate that flies
Shout Out / The Avengers (2012)