I'll just paste my response to this from another site this came up on.

Wow. I'll just state one thing about the video...

They try to prove a plane crash leaves very visible remains when it crashes by showing pictures of other crashes. Well, guess what. Most crashes, and likely all shown had a trained pilot trying to guide the plane to safety. So if there is a way to slow the plane down, it will happen. If there is a way to level it out and try to prevent a direct impact, it will be done. These types of efforts result in less damaging crashes, and might (slim chance) allow for survivors.

The attack on the Pentagon was exactly that, an attack. No attempts to slow down, so the plane will not leave any big pieces behind. The planes in NYC left no huge chunks behind like what was shown in those photos, and they hit a softer building.

Thats just the biggest flaw I saw. Most others will probably be covered by others.

And they never attempt to answer why. Why would the Pentagon hide what happened? Where is the gain? And if it was a cruise missle, where did that come from? Where did the plane go that was still being tracked by radar up until the impact and visible to probably thousands of people, many not even part of the government. Radar and plane tracking systems for planes are monitored by many civilians across the US.

I also have a friend who worked IT at the Pentagon when it happened. Not that saying that will mean anything to the tin foil wearing folks, but getting his story was very interesting.

I also find such claims like this one being the equivalent of spitting on the graves of the people who died that day.