Actually when we captured Ramsey Yousef in the Philiphines (an Iraqi agent operating with Al Qaeda?!?!?{GASP!}) in 1995, he had files on him of the possibility of using Airplanes as airborne missiles, and his target was the CIA building. By 1996, an intelligence memo was put on Clinton's Desk stating that suicide bombings was a possibility, and that security should be set up to prevent it. I believe it was turned down because this would mean shutting off the cockpit, and cutting off the possibility of negotiating with the hijackers.
Overtime, it was largely forgotten about until 9/11 and everyone started retracing their steps. Unbelievably, this often used as a smear on President Bush. He probably didn't even know about this Intelligence memo before 9/11 while Clinton deliberatly ignored it.
I tried to find a source for this info but all i got was conspiracy sites. At one time i saw this documented legitamately but i dont know where.