When Steve asks the Howling Commandos to go back to the front with him, two of them, Jones and Dernier, converse in French and they're sitting awfully close to each other. Makes you wonder what else they use that for...
A lot of the lines between Stark and Banner sound kinda flirty, and a thousand fanfics were launched in the single moment when Stark randomly pokes Banner in the stomach and Banner just puts up a mild, vaguely amused, "Oh, you" type of protest note On the gag reel, RDJ pinched Mark Ruffalo's butt instead; hilariously, it actually didn't require them to play the scene all that differently. Couple that with the scene where the Hulk saves Iron Man twice in rapid succession, and the fact that these two are the only two members of the Avengers to hit it off the instant they meet...
Stark: Finally! Someone who speaks English.
They are seen driving off into the sunset together at the end of the movie.
It's toned down in the movie proper, but the featurette included on the DVD shows that Tony is a little... excited about the Hulk.
Perhaps it's less suspect in Asgard, but the way Thor cupped Loki's cheek and neck while asking him to come home seemed a bit affectionate(in a not so brotherly manner) to mortal audiences.
Their lips were mere inches away◊ from each other when Thor pulled Loki out of his seat on the jet.
Cap and Thor; that searching look Thor gives Cap when Cap goes on fighting after he's hit...it's like a light went on inside his head. Fan fiction appeared for these two months before the movie was released, but that moment helped make it less of a niche pairing.