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.
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.
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.
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.
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.
Rogers emerging from the SHIELD building into the middle of Times Square, where he's inundated by the noise, traffic, blazing neon advertisements and crowds of a new century, is reminiscent of Adam Adamant's equally-stunning Fish out of Temporal Water emergence from the hospital into 1966 London.
The old lady with a submachine gun who works as the "gate guard" into the secret Brooklyn facility and tries to stop an enemy from escaping, is a nod to a similar character in Goldfinger. Unlike the old lady in the Bond film, it doesn't go well for the one here.
◊. 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.
