Another one... or two
In 1996's Independence Day, the giant alien ship hovering
over NYC aims its power beam directly on the Empire State
Building, utterly destroying it, but after the attack the WTC
can be seen with its tops smoldering and wrecked, though
not knocked down:
http://www.sciflicks.com/independence_day/pictures.html
And in the original plan for the first Spider-Man film, our
hero was going to capture a helicopter full of bad guys by
spinning a giant web between the two towers. Once again,
9-11 changed that cool concept.