EASTER EGG #1
When Agent Coulson calls Tony Stark in Stark Tower, Stark says that he has reached his Life Model Decoy which is an obvious reference to the LMD's of the Comics that Fury has used on numerous occasions.
EASTER EGG #2
When Selving is working on the Tesseract, he asks how Clint was able to get these scientist to which he responds that SHIELD has enemies. Reference to AIM maybe?
EASTER EGG #3
At the end of the film, the Other says that for Thanos to go after humans would be to "court death", which directly references his attempts to literally court Death of the Marvel Universe.