In the January 2009 issue of the "Journal of Air Transport Management" there is a useful article on the possible impact of the EU's Emissions Trading Scheme (ETS).

It looks at the options for (in particular) long-haul airlines based outside the EU reducing their ETS costs by making a stop on the way.

For example, if Singapore Airlines flies direct from Singapore to Frankfurt, it will effectively pay an emissions charge for the entire flight. If however it flies via Zurich or Istanbul, it will only have to pay the charge for the shorter legs - between Zurich and Frankfurt or Istanbul and Frankfurt. So the ETS cost/passenger will be about 15 - 18 Euros less for those routings.

The article also shows the relationship between flight distance and the distance the aircraft actually flies at cruise altitude - its most efficient altitude.

For flights between 188 km and 312km, the aircraft is only at cruise altitude for 21% of the time. The rest of the time it is either climbing or descending. Between 313 km and 437km, it's at cruise altitude for 30% of the journey: this increases to 40% for flights between 563km and 687km. At 876km, it is 45%.

So only on relatively long journeys - where time makes flying competitive with rail - does an aircraft fly at cruise altitude for more than half of the time it's in the air.