On Native Soil
There is a poster for a 1995 movie called The Last Word that has the WTC's in it. However, the poster is titled Cosa Nostra: The Last Word. It is viewable on IMDB.
The WTCs are also on the poster for the movie Funny Valentines from 1999. This can also be seen on IMDB.
Lastly are some shots from the movie Shock and Awe.
There are various 9/11 tv footage shots between 9.45-11.33. There are a couple of WTC shots but mostly just the immediate aftermath after the towers came down.
Somewhere between 34-35min in, there is an ad on tv for a show called Video Music Box and it has the New York skyline on it with the twin towers.
There is (blink-and-you-miss-it) 9/11 footage at 6min 15sec.
*A Futile and Stupid Gesture
Around 19min and 49sec, there is a backgorund shot of the twin towers being built. There are 2 shots in this scene.
There is another shot of them at 1hr 20min. They are fully built at this point.
The Reluctant Fundamentalist
Shots in the movie:
Various 9/11 shots between 42.07-42.28
Various 9/11 background footage shots between 54.18-54.43
9/11 rubble at 1hr 22min 9sec
The German poster for that movie has the WTCs on it.
It's called Im Bann Des Terrors.