I've attempted to compensate for the carbon emissions resulting from our recent flights to Greece and Denmark by funding a proportionate amount to sustainable energy and reforestation projects. I used an Oxford-based organisation called Climate Care, recommended by Nick, who neutralised the carbon output of his stag weekend to Barcelona, G8-style.
Climate Care have good online CO2 calculators and an impressively detailed algorithm for determining the emissions from air travel:
"In summary, for long haul we take the average fuel burn figures for a Boeing 747 and an Airbus A360 as published by the EU. We divide this by the average number of seats (not occupied seats) and also subtract the amount of freight carried by the average long haul aircraft. We double the amount of CO2 emitted to take account of the enhanced atmospheric impacts of aviations. We then calculate the great circle distance between the airports in question. A similar method is used for short haul, except that we use a Boeing 737 as the reference aircraft."
It's not clear how this tonnage figure is monetised, or how the carbon sequestering effects of their projects are calculated, but on the whole Climate Care give the impression of an organisation doing the right thing.