http://www.slate.com/blogs/the_slate...t_spotted.htmlThe effect of turning off the transponder is to make the aircraft inert to secondary radar, so civil controllers cannot identify it. Secondary radar interrogates the transponder and gets information about the plane's identity, speed and height. It would however still be visible to primary radar, which is used by militaries.
One question....would passengers be able to text or email, would that be picked up anywhere? (Or would the hijackers turn off the wifi or whatever?) Because it sounds like the plane made a drastic change in course, probably under duress (whether mechanical or human-made), and flew in a different direction for at least an hour.