I know a lot has been said about the ramifications to the MCU and Agents of SHIELD in light of the events in Captain America: The Winter Soldier, but why aren't we talking about how the big reveal from this movie affects the earlier movies?
We now know that Hydra has been a major part of SHIELD since right after World War II. This may explain some of the things that we have seen in some of the pre-TWS movies. Let's start with Iron Man 3.
Many people have wondered where SHIELD was during the events of Iron Man 3. The Mandarin and his Ten Rings terrorist organization appear and start wrecking everything, but only Tony Stark shows up to face him. This seems like the exact sort of event that Nick Fury and his organization would be all over. Maybe they didn't respond because Hydra was behind the entire thing. Arnim Zola explains that Hydra is all about fostering chaos to prepare the world for a time when they are ready to accept Hydra taking over. Allowing Aldrich Killian and his company AIM to develop Extremis and terrorize the world seems to be right in line with the Hydra mission statement. After all, Hydra and AIM have a history of working together in the comics. So Nick Fury sees the rise of the Mandarin as a threat, but is told to stand down by his superiors because they are Hydra.
The events of TWS also have impacts on the first Avengers movie. The movie opens with SHIELD studying the Tesseract much like Hydra was doing in Captain America: The First Avenger. It is later revealed in the film that SHIELD has been making weapons using the power of the Tesseract which is exactly what Hydra was doing in World War II. Fury argues that the weapons are necessary because of the way the world is now, but it is more likely this is just what he believes and the reality is that Hydra just picked up where they left off once SHIELD rediscovered the Tesseract. Once the Tesseract is stolen by Loki the council that Fury answers to initially doesn't want to bring together the Avengers to stop Loki. Maybe they see the formation of this group as a great threat to Hydra. The same council is also very quick to use a nuclear weapon to destroy New York City and stop the Chitauri invasion. Even though there is no guarantee that the detonation would close the wormhole, this type of destruction would surely cause the exact type of chaos that Hydra seeks to inflict on the world. They even manage to have the missile launched from aircraft right on the Helicarrier without Fury's authorization.
Can anyone think of anything else?
EDIT: I forgot about Senator Stern! Senator Stern is in charge of the hearing at the beginning of Iron Man 2. He is desperate to get control of the Iron Man armor and now we know why. Hydra would love to have that technology.