Reinforce the doors to the cockpit, put a couple of armed guards just outside them. As iocane pointed out, you may want to replace their guns with weapons designed not to puncture aircraft, such as electro-stun and sleepygas.

Have a panic button in the cockpit and just outside it that does the following:

  • Closes and locks the doors so that they cannot be opened until after the plane has landed.
  • Notifies Air Trafic Control.
  • Give air trafic control the option to take control of the plane remotely. This is harder, and may not be neccesary. I don't see this option being feasable right now for passenger craft without it being deliberately engaged by both sides, and only as a backup to the pilot - an emergency measure rather than the norm. Maybe someday, after years of using remote piloting for unmaned craft and proving it's robustness, we'll be ready to routinely entrust our lives to unpiloted aircraft, but not yet.

Or an even more cautious approach- divide the plane into 3 sections:
The passenger section is largest, takes up all except the front of the plane.
The crew section is in front of that, seperated from the passenger secion by a reinforced door.
The cockpit is at the front, seperated from the crew section by a second reinforced door.

Both doors should be kept closed unless they need to be opened. Unauthorised persons entering the crew section should be cause for alarm. The system should ensure that the two reinforced doors cannot both be opened at the same time, or even just after each other. Thus the cockpit cannot be rushed and there is always time to press a panic button.

Put armed guards outside the cockpit door, right next to the panic button. Make sure that the people in the cockpit have a CCTV view of the crew section just outside, so if they see problems they can press the panic button instead of allowing the door to open. The guards may want similar CCTV views of the passenger section.

I would not suggest a bulkhead or cockpit door that can only be opened from the inside, as you need to make sure that in case of say, one pilot being out of the cockpit to relieve themself and the other having a heart attack, the crew can always still get back into the cockpit. Unless the panic button has been pressed.

Short of sedating or shackling all pasengers on all flights, there is no way to totally prevent the posibility of a passenger suddenly grabing another passenger or crewmember and threatening their life. However it is posible to prevent this from turning into control of the plane, or even leverage over the course of the plane.

In the past, giving the hijackers acess to the cockpit and allowing the posibility of an uncheduled trip to Cuba was seen as a lesser evil. In since 11 September 2001 This is clearly no longer the case.

Finally, a foreign policy that does not cause resentment and anger in large parts of the world would alleviate the need for such measures.

Update, December 2001. is today airing a serious proposal. The suggestion is that of virtual no-fly zones. This is software in the airplane's navigation system that steers the craft out of designated areas. It would feel like "soft walls" that increasingly push the plane away. So it literally cannot fly where you it is not supposed to. An argument use in favour of this is that the pilot retains more control than with some of the remote control proposals.

In general, I guess we are going to see much closer attention paid to aircraft that are not following their expected course, and stronger external measures taken against them. This may include onboard or remote methods of steering the craft back where it is supposed to be.