The main theory I've been told from people who work in aviation is that the pilot (or Co pilot) waited until the other left the cockpit. He then locked the door. Removed airpressure from the cabin to knock everyone out. Turned off his transponder (the thing that tells everyone where you are). Landed the plane on the water and let it sink. This would explain why there is no trace of it. Everyone on board would be knocked out and the plane would have landed and sank in one piece.

Supporting evidence: you can't turn off the new transponders being put in airliners. They have the button but they keep sending a signal. This is all being done quietly though so few people actually know about that bit.