1. Avengers tower reference when HYDRA was locking on to their targets. Also, presumably the person inside the tower being targeted was Tony.
2. Bruce Banner and Stephen Strange references.
3. A reference to a school valedictorian (Gwen Stacy)?
4. When Cap visits the museum and watches the Peggy Carter footage, she mentions that Cap saved the life of the man who later became her husband. I think that that's a Gabe Jones reference.
5. "Who the Hell is Bucky" line.
6. Howard/Maria Stark references.
7. Pictures of Peggy, Howard, and Col. Phillips in the old SHIELD bunker.
8. Multiple Howling Commandos references at museum.
9. Reference to crappy 90's Cap movie (BW asking where he learned to steal cars).
10. Reference to Agent Carter one-shot (Cap mentioning that Peggy helped to found SHIELD).
11. Cameos by Peggy, Arnim Zola, Senator Stern, Baron von Strucker, QS, and SW.
12. Loki's scepter from Avengers.
13. Sharon Carter name-drop at the end.
14. Maria Hill going to work for Stark Industries.
15. Nick Fury faking his own death (shout out to the comics).
16. Red Skull mention.
17. Reference to Zola's robot body when he's on those monitors.
18. BW working for the KGB (comic book reference).