This is my list of every anime that depicted the New York City WTC Twin Towers contemporaneously. That is, only including anime from 1973 to 2001. This is not about 9/11, this is about documenting how anime portrayed one of the most iconic city skylines while it was still around.
However, I believe this list is not complete. If you know of any anime that show the twin towers, please let me know so I can add it to the list. Some of these are easy to find; if they are tagged as taking place in New York on AniDB then it’s a quick skim through the show/movie to look. However others, like the Kimagure Orange Road movie, are much more difficult.