Why not remove the pilots and the cockpit altogether? All commercial passenger aircraft could be flown remotely from the ground and then there's no possibility of a hijacker threatening the pilots or taking over the controls.
On the other hand we could try to avoid kneejerk and/or extreme reactions. It would be easy to over-react in this instance because of the sheer scale of the loss of life and destruction, however, I agree with Danny in his early post that the most effective way to deal with this threat is to prevent would be hijackers from gaining access to aircraft in the first place. These were four aircraft out of the many thousand commercial flights worldwide each day. Each was an internal US flight where for many years security has been notorious for its laxity compared with international flights. Hijacking on international flights is almost non-existent and despite the horror of what happened on Tuesday the scale of any future threat and the answer to it should be assessed in a calm and rational manner. Increased security on internal flights is likely to remove the risk of such an incident occuring with a comemrcial passenger aircraft in the future. Unfortunately it will not remove the likelihood of other terrorist atrocities continuing in the future.