Video: Shot of two towers burning from street level -- 6m06s Google Video. More on this video here

The following flashs are made from a snippet of the above sourcefile.

This could be a bird - or a missile. There was numerous reports of missiles fired against the World Trade Center. Here are some of them - Fire and missiles/rockets.

PAPD OFFICER:
Advise (Inaudible)… there is something … looks like a missile coming out of the wall of the (Inaudible) … the second building."

Given that the video resolution is not that good it could be a bird, and there seems to be some video artifacts some places. But given that it looks like the objects is hitting WTC-1 on the east side. It continues through the building and becomes visible on the other side of WTC-7.
The object doesn't seems to leave any traces on WTC-7, but due to the objects speed and low video resolution, it could be there.

On the other hand the object seems to fly in a complete straight line and the travelling lane/angle doesn't look typical birdish, but this could be an optical illusion. If the object is going behind WTC-7 it cannot be a bird, then it is to big and too fast. On the other hand it's kind a strange that the object would continue through WTC-1.
Anyway - if you know of a better version of this video let me know.