A few years off, but post 2012 airlines will have to buy carbon credits for any excess carbon emissions for flights in or out of the EU. Or at least that is the latest law that the EU parliament is set to sign.
http://www.reuters.com/article/envir...52778920080627
Airlines with newer, more efficient aircraft should be in a better position as credits will be on a cap and trade basis using 97% of average emissions in 2005/6.
You can be sure that airlines will try and pass any costs incurred to passengers, probably as a carbon surcharge.