The best way is a CO2 gas chamber. there are a few ways to make one (using a CO2 gas cylinder or using dry ice) Here are some DIY's

Dry Ice: http://ball-pythons.net/forums/showt...and-Humane-too

CO2 Cylinder: http://ball-pythons.net/forums/showt...Y-CO2-chamber)

The most important thing is to start off with a little gas to put them to sleep first, then flood the chamber to kill them. if they are awake when you flood the chamber with gas it won't be painless.