If you haven't seen the episode, you must know the episode is pretty much _about_ the Twin Towers. The entire plot revolves around them. Barney (on a bender, of course) has parked Homer's car between the Towers (the writers and animators took some liberties with the layout of the World Trade Center) and Homer has to retrieve it before the City disposes of it themselves (they also took liberties with the generosity of NYC parking violations enforcement!).
Lisa: "Dear motorist, your vehicle is illegally parked in the borough of
Manhattan."
Homer: My vehicle!
Lisa: "If you do not remedy this malparkage within 72 hours, your car
will be thrown into the East River at your expense."Literally a third of the episode takes place at the foot of (and inside) the Towers. One of the funniest sequences in the history of _The Simpsons_ is Homer's quest for food and drink, immediately followed by his need to go to the bathroom, all while having to keep an eye on his car so he doesn't miss the policeman who's coming to unlock the boot on his tire. The sequence includes, aside from the now-legendary "Flushing Meadows" dream sequence, a trip up and down the elevators of both Towers. There are apparently two short WTC scenes cut in syndication; fortunately I have it on tape in all its glory.
(The comprehensive episode capsule is at http://www.snpp.com/episodes/4F22.)
It would be a shame to permanently cut this episode out of broadcast. It is one the greatest episodes of the funniest show on television (or at least it was the funniest show at the time). If anything, the episode is a great tribute to New York City.