You hear it all the time, even from people who should know better: September 11, 2001 was the only time in history that all air traffic in the United States was halted.
Air & Space researcher Roger Mola was the first to point out that it wasn't the first time. That distinction goes to Operation Skyshield, a training exercise conducted 50 years ago today (see Mola's article from our Feb/Mar 2002 issue). A NORAD-run test of defenses against Soviet air attack, Skyshield was the largest aviation exercise ever held. On three occasions from 1960 to 1962, all U.S. commercial air traffic was canceled while thousands of military aircraft pretended to go on bombing runs over major cities including New York, Chicago, and Washington.
Mola is currently working on a documentary about Skyshield. See his preview of the work-in-progress here.