The Sydney Morning Herald recently carried an article entitled High altitude flights spark symptoms. It referred to a study of the Effect of Aircraft-Cabin Altitude on Passenger Discomfort published in the New England Journal of Medicine. The study found that the reported rates of discomfort increased greatly at simulated altitudes above 2100 metres and durations between 3 to 9 hours. The onset of acute mountain sickness did not appear to depend on the altitudes studies (between 198 to 2438 metres) in those that experienced it (17.4%).
I believe that I experienced altitude sickness on flights with Malaysian Airlines and Asiana with severe headaches and nausea that improved upon descent to lower altitudes. It is interesting that this did not occur with all airlines (eg Qantas, Cathay Pacific) leading me to suspect that some airlines cycle cabin air more often (perhaps affecting the oxygen and carbon dioxide ratios) or keep their cabin pressure lower (although the study would seem to discount that). Both strategies save fuel.