Easter Eggs fit into the Marvel Universe just as well as Mutants, irradiated spiders, or Avengers. There are hundreds of issues of storyline to fit into each movie and there's simply no way to do it.
The absolute best way to please both the diehard comic fan and the casual movie-goer alike is to sneak in these deep geek nods to characters and things that may not directly work on screen. Easter Eggs are also a clever way to tie a universe together (sometimes seperate universes in some cases do to copyright.), or to foreshadow or throwback to prior movies without seeming redundant.
Simply put easter eggs make comic movies better, (just don't overdo them Iron Man 2!), and ALL the studios handling the different heroes in the Marvel Comics universe know it to. So take a peek at some great little moments you may have missed, then rewatch some of these amazing movies in a whole new way!
http://www.ranker.com/list/all-easter-eggs-from-marvel-movies/ranker-comics,
Pulp Fiction Exists in the Marvel U - Iron Man 3
Jon Favreau's Happy Hogan's bodyguard attire in the Flashback's is exactly that of Vincent in Pulp Fiction.
Crossbones Is Born - Captain America: Winter Soldier
A mercenary of Cap's archenemy, The Red Skull, and of Hydra, Brock Rumlow makes his first appearance in Winter Soldier. By the end not only is Crossbones charred to a crisp but his criss-crossed gun straps make for a pretty great translation of his comic costume.
Remy Lebeau - X2
Gambit's real name appears as Mystique hacks the computer in X2, along with many, many others.
Rhodey's Ringtone - Iron Man
When Tony calls James Rhodes in the first Iron Man his ringtone is the theme to the 1966 "Iron Man" cartoon. The theme actually pops up in different variations throughout the series in clever ways.
Pulp Fiction Exists in the Marvel U - Captain America: Winter Soldier
Nick Fury's Tombstone reads, "The Path of the Righteous Man, Ezekiel 25:17" which is the same speech Samuel L. Jackson preached before killing motherF%c$er's in Pulp Fiction.
Creator Cameos - X-Men Days of Future Past
During Bolliver Trask's address to congress both Len Wein and Chris Claremont are amongst the crowd.
(Len Wein pictured)
Pieces of Movies Past - X-Men Day's of Future Past
Pieces of Mutant history (and film history) surround Magneto's helmet as he goes to retrieve it, including the coin that killed Shaw, Havoc's chest piece, and one of Angel's Wings.
Terminator Nod - X-Men Days of Future Past
As a specific homage to Terminator, when Wolverine travels through time he ends up on the other side just a buck naked as Arnold did on his time traveling expoits.
Cap's Shield - Iron Man
In the first Iron Man, Captain America's iconic shield can be seen in the background being worked on.
Quicksilver's Lineage - X-Men Days of Future Past
When Quicksilver discovers Magneto's power set he says "You can control metal? My mom knew someone who could do that." In the comics Magneto is Quicksilver's father.