In Level 9, "Doctor in the House", Mr. Fantastic uses himself as a parachute. He then says "I saw this in a movie once."

This is a reference to the Pixar film The Incredibles, in which Mrs. Incredible uses her powers in a similar fashion.
Contributed by Doctor Ink
In the Deadpool mission "House Party Protocol" when you Spoiler:build the DJ booth Nick Fury says "And you will know I am the DJ when I lay my beats down on you.", this is a reference to a line in Pulp Fiction where Jules Winnfield quotes Ezekiel 25:17; "You will know my name is the lord when I lay my vengeance upon thee."
The actor Samuel L. Jackson played both Jules Winnfield in Pulp Fiction and Nick Fury in the ##Marvel## movies.
Contributed by Epicwolf13
At the begining of Level 7, Thor opens a portal to the Bifrost, and the characters are sent flying through a wormhole which greatly resembles those The Doctor travels through in the fourth season of Dr. Who. Further reinforcing the reference are several blue phone booths also travelling through the wormhole, which resemble The Doctor's TARDIS.
Contributed by Boyobmas
The achievement "Don't I Know You?", which is obtained by controlling both Captain America and Human Torch in free play, is a joke about how Captain America and Human Torch were both portrayed by the same actor (Chris Evans) in Captain America: The First Avenger and the Fantastic Four films, respectively.
Contributed by Tbeasom26
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Shortly after his introduction, the Human Torch comments that a certain bridge looks like a rainbow road, and it makes him want to race. This is likely a reference to the Rainbow Road seen throughout the Mario series, primarily as a racing track in the Mario Kart games.
Contributed by Tbeasom26
While playing as Spider-Man, leading up to the boss battle against Venom, Spider-Man will exclaim that enemies are "coming out of the walls!" This is likely a reference to the famous line from the 1986 film "Aliens".
Contributed by Dazz
In the basement of the Helicarrier, a character will ask the player to help them clear out some snakes, saying,

Snakes. Why'd it have to be snakes? Hate them! How'd they even get on board? Director Fury told me specifically to "get these snakes off this god-darn Helicarrier." I may be paraphrasing slightly. Anyways, can you help me out?


S.H.I.E.L.D. Director Nick Fury's appearance in the Marvel Ultimate line of comic books was based on Samuel L. Jackson, and he has played the role in a number of Marvel movies. Samuel L. Jackson also played the part of Neville Flynn, an FBI agent in the film "Snakes on a Plane", in which he exclaims, "That is it! I have had it with these mother-fucking snakes, on this mother-fucking plane!"
The opening line is also likely a reference to Indiana Jones, with the same line appearing in the 1981 movie, Raiders of the Lost Ark.
Contributed by Dazz