There used to be a series on Youtube called "9/11 in Hollywood" which ended up growing to 26 parts after several viewer submissions. It investigated in detail these types of references (including most of the ones mentioned here) in film. The series went a little overboard (as in, including every image of a clock in a movie where either hand was pointing to the 9 and the 11 at the same time), but there were enough interesting coincidences to make it worthwhile, imo.
As I understand it, the series was removed long ago due to copyright issues, but it is still available on various torrent sites. I grabbed my copy from _concen.org about 6 months ago, and it was definitely interesting to watch. Not sure where to currently obtain a copy, but if there is an interest, I could burn it to a CD or some such.