I'll start:
whilst I believe that the two movies do carry some interesting material, I have to ask myself certain questions....

Against the conspiracy:

• this would have to be the best-kept secret EVER; too many people would have to know something and be involved - is that possible?
• the loss of life. If this was from the Bush administration, that is taking Friendly Fire to a new level
• I saw the second plane hit live on CNN. That will stay with me for ever

For the conspiracy:

• the collapse of WTC1 and 2 with reports and visible explosions make no sense to me given the facts and my underlying knowledge of what I would "expect"
• WTC7. Again, how and why? It seems a valid question
• Pentagon: you have to say what hit it.
• Cellphone calls - some accounts of course hearsay but those accounts do hint at scripted conversations
• Flight 93 - did it go down, did it land?
• Why not release the CCTV footage from the hotel and gas station near the Pentagon?

I have also discounted the mixtures of eye witness reports - with the associated trauma, speed of events and other factors, the reports of small passenger planes, windowless planes and so-on do not add clarity for me.

More to come; I'm editing and reading Wiki!