There are many laws and regulations governing what may and may not be put up in the air because of the obvious safety concerns, and indeed it would be very foolish not to stay within them. Balloons seem a far better candidate for upwardly mobile Raspberry Pis than planes.
Here is some info on how FAA regulations affect amateur balloons and their payloads in the US: http://vpizza.org/~jmeehan/balloon/
-- see the section "Regulations", 4th section down. (There's a link to the full FAA doc there too.)
If you ensure that your balloon-based Rpi project masses under 4 lb (1.8Kg) and is attached to the balloon by only the flimsiest of cords, it would seem that it's "clear skies" for Rpi balloonists in the US.
If anyone has similar information for the UK, I would be most interested to read it.