OK, disclaimer up front. I am emphatically not a conspiracy theorist and I'm not claiming that the events of 9/11 were anything but the act of 19 hijackers. In fact, I'd downloaded the Tracker Video Analysis and Modeling Tool and was looking for video to utilize to familiarize myself with the software. I downloaded a high resolution video of the North Tower collapse to see if I could dispel the notion that the towers had fallen at a free fall velocity as claimed by the conspiracists, unimpeded by the piston effects of air in the buildings, structural and non-structural building elements, etc. In this, I was arguably successful:
This is the plot of the "y" position of an identifiable spot on the antenna atop the North Tower at the start of the collapse and followed for about 2.25 seconds. Fit to a parabola, the "a" parameter should be the 0.5*g in the term s=0.5gt^2, the equation for gravitational acceleration. For free fall, "a" should be 16 (this was done in feet and g=32 ft/s^2). The -12.2 would indicate an acceleration of 24.4 ft/s^2, implying that there is an upward vertical force acting against gravity, consistent with the factors mentioned above.
All well and good (though I'm certain that it's unconvincing to the conspiracy sector), but then I looked at the video linked above. My initial motivation was to chuckle at the silliness of some of the videos, and this I did. In the case of the linked video though, I have to concede that while I'm unwilling to agree that it is proof that the Towers were not hit by hijacked civil airliners, I also cannot explain its key elements to my complete satisfaction.
I'm certainly interested in any deeper analysis and possible explanations for what seem to me to be anomalies. The best I've seen in explaining the points raised is in this video, part of a series entitled "9/11 Debunked" and subtitled "Debunking every single 9/11 conspiracy theory, one at a time." But there's nagging doubt as to whether this is the explanation.
Regardless, the inability to explain every single detail in such a complex chain of events is certainly not sufficient to posit an inside job.