Iron Man was pretty much an update from his first issue where he got kidnapped by Communists but the basics were the same up until he got home. Stane was actually a rival industrialist not basically his uncle. SHIELD did form around the same time as the comics we know and love did start though.
Winter Soldier was a two fold thing with the Bucky being the Winter Soldier being the first part and later on a few years after that it was revealed SHIELD was born from HYDRA.
The Thor movies were kind of a mishmash of a bunch of different storylines. The Destroyer armor, Loki trying to kill him (repeatedly) and everything else happened a lot over the years. Although Thor being banished due to arrogance and to learn humility was pretty much the reason for the Thor comics in the beginning especially with the call back to the Donald Blake identity from the first movie since he was a doctor who only found out he was Thor during a trip to Norway when he got attacked by (and this is a real thing from Marvel) the Stone Men from Saturn. The showed that in the Planet Hulk movie except it was with Beta Ray Bill instead.
Avengers was sort of based on two versions of Avengers showing up in it. The first being the Avengers coming together to battle Loki in Avengers #1 even though it didn't have Ant-Man or the Wasp and had Captain America even though he didn't show up until issue #4. The other Avengers were the Ultimate Avengers who were all jerks. They had to deal with the Chitauri being shape shifting aliens doing a slow conversion/invasion of earth for decades.
Iron Man 2 was part of a few storylines where Stark was dying and had to face his own mortality. We also got Hammer who was a big jackass in the MU creating a lot of different super villains for industrial sabotage and just to piss off Tony. Whiplash is more of a combined (I think) Titanium Man and Whiplash due to the Russian genius part added.
Captain America TFA is basically just WWII Cap kicking ass, so no storylines needed.
Incredible Hulk is another mash of a few stories. He meets up with Betty after being on the run, Blonsky turning into the Abomination and Ross basically committing mutiny and attacking Hulk with armies and secret forces is basically every couple books.