Battle Scars introduced Nick Fury, Jr., the black son of the original Nick Fury. The new Nick Fury is very obviously based on Samuel L. Jackson's portrayal of Fury in the live-action movies, which was itself heavily influenced by the Ultimate Marvel version of the character. The new Nick also lost his eye, and as time has gone on he's slowly assumed the role his dad used to have in the comics.
After Avengers Tower was destroyed during Fear Itself, it was rebuilt with a new, more movie-inspired design in the first issue of the 2012 Avengers Assemble comic book series.
In an extremely controversial example, Marvel used AXIS to reveal that Quicksilver and Scarlet Witch aren't really the children of Magneto, mirroring their depiction in the Marvel Cinematic Universe (where Magneto couldn't be used thanks to rights issues). Their powers were also retconned into being the result of scientific experimentation like in Age of Ultron, instead of naturally occurring mutations (ironically WandaVision later revealed Wanda's powers are natural and the experimentation merely enhanced them).
The comic version of S.H.I.E.L.D. adopted the Avengers Initiative from the MCU. The second volume of Secret Avengers saw S.H.I.E.L.D. using the Initiative to recruit its own team of superheroes, similar to the origin of the Avengers in the live-action film.
S.H.I.E.L.D. and the Avengers have been seen using Quinjets based on the models used by S.H.I.E.L.D. in the movies.
Hawkeye began wearing a black leather costume similar to the one he sported in the first Avengers film. The movie costume was itself inspired by the one seen in The Ultimates, though the Earth-616 version added in some purple coloring.
If one thing has stuck (besides the return of adult Tony and normal-looking Wasp), it's Tony sporting a beard in addition to his mustache. It's become so linked to the character that many recent incarnations, including the Ultimate Marvel and Marvel Cinematic Universe versions, have had Tony with it.
While it could just be a coincidence, when the Ultimate Marvel imprint decided to re-imagine the Avengers into The Ultimates, it reused the idea originally presented here of S.H.I.E.L.D. helping to set up the team. The Live-Action Adaptation of The Avengers reused the idea, though it was likely inspired by The Ultimates.
In HR, an LMD of Nick Fury lied and said Captain America was "deactivated" by President Truman after a disagreement over the use of atom bombs against Japanese civilians. Chuck Austen tried to integrate this idea into the mainstream continuity during the controversial "Ice" story arc, where it was revealed that the government had Cap frozen so that he couldn't stop the atom bombs from being dropped on Hiroshima and Nagasaki. Of course, the story was so reviled that it was later rendered Canon Discontinuity, but still...
In classic canon, Tony Stark and Bruce Banner do not like each other at all. In Heroes Reborn and going through quite a few versions, like the MCU, they're friends.
The true face of the original Ultimate Universe Chitauri wasn't revealednote As Darker and Edgier versions of the mainstream universe's Skrulls, they usually appear shapeshifted and nobody knew what they really looked like for ages. Also, being Skrull Expies is why all adaptations' Chitauri, even before the movie, are your basic Alien Invasion and not shapeshifters; Marvel Animation tends to just use Skrulls when it wants Skrulls. until Hunger — when it was shown they look exactly like their movie counterparts.
The Avengers (Jason Aaron) brought forward Avengers Assemble's portrayal of the Squadron Supreme as villains more in line with their counterparts the Squadron Sinister, as simulacrums created by Mephisto, although unlike the show's version, Nighthawk would have a Heel–Face Turn much like the original Squadron Sinister Nighthawk had.
