Captain America: The First Avenger / Shout Out

The opening scene of an apparent Flying Saucer buried in the Arctic ice is similar to The Thing from Another World, though lighted poles instead of people form the shape of the craft under the ice.

Like another Marvel superhero's movie, Cap sticks a bomb into a tank and then has a slow motion cut of him moving away as it explodes behind him. Unlike Iron Man, however, Cap is on top of the tank while he's blowing it up.

This poster◊. You know what it's a shout-out to. This also counts as a shout-out to one of Joe Johnston's earlier works, The Rocketeer.
Upon gaining the Tesseract/Cosmic Cube at Tønsberg, the Red Skull remarks that Hitler is digging around in the desert for trinkets. Perhaps Schmidt's talking about Hitler seeking the Ark of the Covenant? Which in itself is a Truth in Television, as the Nazis often tried to seek out occult artifacts in their plans for World Domination, often sending out the Thule Society and the Ahnenerbe for expeditions and experiments involving these occult artifacts. There are also two thematic references to the "he chose poorly" scene from Indiana Jones and the Last Crusade: firstly when Schmidt is clever enough to realize that the Cube hidden in plain sight must be a fake and works out where the real one is hidden, and secondly when Rogers chooses the simplest of the shields.

At one point during the final battle, a HYDRA guy ends up getting shredded by an airplane propeller, just like in Raiders of the Lost Ark. Unlike the original though, we actually see what happens. It goes a step further; both mooks were shredded by the prop of a German flying wing aircraft.
Yet another reference to Raiders of the Lost Ark, after grabbing a artifact of the gods, Schmidt gets melted.
The motorcycle chase through the forest acts as a double Shout-Out to the bike chase from Indiana Jones and the Last Crusade and the speederbike chase from Return of the Jedi. One presumes that's why the bike chase scene features a prominently-placed Wilhelm Scream.
This isn't the first time a key part in a person's plot to overthrow Adolf Hitler was named Valkyrie (although the person in question this time had an evil motive, unlike the real life and movie version). This doubles as a reference to the fact that Skull is using power from an Asgardian artifact. And for a bonus reference, the Valkyries' job in Norse mythology was to choose who lived and who died in battle, rather fitting for a plane designed to bomb the entire planet.
- While we're on the subject, there is an extremely Cool Plane in Real Life, also named the Valkyrie, and also initially designed to lay waste to entire cities.

The repeated references to "bullies" and how "it doesn't matter where they come from" are clear references to Jack Kirby's reason for creating Cap in the first place: I know a gangster when I see one! Changing the jargon from "gangster" to "bully" could actually be considered an improvement on an already awesome point — bullies, gangsters, Nazis... they're all just thugs who hurt people For the Evulz.
A non-comics shout-out by the prop guys: One of Stark's shield prototypes is clearly the classic RX-78-2 shield.
Howard Stark is clearly based on both Real Life and The Aviator Howard Hughes. First by his given name, then by being a brilliant aircraft engineer and pilot, inferred he is wealthy enough to not care about risking his career, being a renowned ladies' man, last by his physical◊ appearance◊. This is extremely apt, because Tony Stark was originally based on Howard Hughes.