One could also say that it was predicted in "The Dark Knight Returns"* and an issue of Spider-Man**.
Spoilers, of course.
*In DKR, at first Two Face tries bombing the twin towers. A while later, after the nukes, a plane crashes into a tower that looks a bit like the aforementioned Gotham twin towers.
**In one issue of Spider-Man, Juggernaut pushes the WTC over. Seriously.