I was bored on one flight and so I actually wrote a quick and dirty simulation while on the flight: http://blog.chewxy.com/2012/04/04/a-better-passenger-boardin... . My main complaint at the time had been the inefficiencies brought about by loading luggage in the overhead compartment.

I was actually quite surprised by the simulation - that queueing people into odd-even queues make for faster boarding.

Caveat: the code I shared on github is actually quite terrible. Ignore the code, look at the pretty charts