Possible Scenario.
I can imagine the co-pilot saying "Good-night" to the air-traffic controllers, then drugging or incapacitating the pilot, and putting the aircraft on autopilot and flying until fuel exhaustion.
Notice that this leaves open various scenarios as to how the rest of the crew and the passengers were disabled. I suppose one could imagine that the co-pilot disabled the pilot, brought the aircraft down to 5000ft, breached the hull somehow - he could have even broken a window in the cockpit - and then had the autopilot fly up to 35000ft (or whatever altitude would be required), killing everyone on board by hypoxia, with the autopilot then flying the aircraft out to sea until fuel exhaustion.
Since there are people here with some familiarity with aircraft operations, I would be interested in hearing their opinions of this.
There was a case in Egypt a few years back where the pilot decided to commit suicide by crashing his passenger jet. MH370 co-pilot could have learned something from that. http://en.wikipedia.org/wiki/EgyptAir_Flight_990.
See also http://en.wikipedia.org/wiki/Royal_Air_Maroc_Flight_630 where a pilot disconnected the autopilot and crashed the aircraft. Also relevant is http://en.wikipedia.org/wiki/SilkAir_Flight_185 .
See http://en.wikipedia.org/wiki/Federal_Express_Flight_705 where a member of the flight crew smuggled a hammer aboard the aircraft, and attempted to bludgeon the pilot and co-pilot to death. He didn't use a gun because he had a $2.5 million insurance policy on which he wanted his family to collect and gunshots in the bodies of the flight crew would make that... problematical. The co-pilot of MH370 could have had a motive to want the bodies not found: insurance policy, sparing his family the shame of having a family member commit suicide, possibly other motives.
Auburn Calloway, a Federal Express employee facing possible dismissal for lying about his previous flying experience, boarded the scheduled flight as a deadheading passenger with a guitar case carrying several hammers and a speargun. He intended to disable the aircraft's cockpit voice recorder before take-off and, once airborne, kill the crew using the blunt force of the hammers so their injuries would appear consistent with an accident rather than a hijacking. The speargun would be a last resort. He would then crash the aircraft while just appearing to be an employee killed in an accident. This would make his family eligible for a $2.5 million life insurance policy paid by Federal Express.