Look at the 27 second mark of this video. It looks to me like there is a tail to whatever hit the Pentagon.
A plane wouldn't leave a tail of fire like that in my opinion. A missile more likely would.

toggle back and forth between 25 sec and 30 sec mark a few times...

http://www.youtube.com/watch?v=t9HrwTONo4k <-- maybe better view at YouTube site.

Let me know what you think. I hadn't looked at it this closely or had the opportunity to see it slowed down like this.

And at the 25 second mark you can see something in the right of the screen.

*noticed this while watching "No End In Sight" on The Sundance Channel.