The best ways are to keep potential hijackers off the aircraft in the first place, limiting access to the cockpit and training pilots and cabin crew in procedures in case of a hijacking or other event.
ElAl, because of their unique situtaion, is the absolute best at reducing all those major areas of risk but is at a level unacceptable to any other airline due to costs, time, facilities and invasions of passanger's privacy. In the meantime, much can be done in simplier ways to reduce the risks.
A properly run TSA
, like seen in many EC
and Asian countries, can have well trained people along with sound and effective procedures keeping off potential troublemakers as well as potential weapons and bombs.
Limiting access to the cockpit, including 2-door or reinforced door systems with coded bypass systems for emergency crew access or access for food and toilet facilites by cockpit crews are already well established on many airlines. Had they been in effect prior to 9/11, they probably would have prevented those terror acts.
While there are limitations at this time on systems to operate a/c remotely in case of a hijacking where the cockpit is taken over, those could be developed over the next several years. In the meantime, there can be training of cabin crew to thrwat acts along with armed Air Marshalls. Pilots can have coded messages from cabin crew to make severe manuvers of the aircraft that will disrupt hijackings early on.