According to Veterinary Clinical Services
, part of the Yale University website, the acceptable methods for reptiles are:
penetrating captive bolt
stunning and decapitation
decapitation and pithing
One thing to remember about reptiles (any cold blooded animal), is that they can hold their breath longer than we could think possible. Since they don't need oxygen to use in making body heat, they can get by with very little by our standards. Holding their breath for ages is nothing to them, but it also means inhalant gasses are absorbed much slower. If it takes a couple of minutes to gas a rodent, a reptile might take an hour or more. Keep this in mind if you decide to use CO2 or other anethesia.
There's also a good selection of articles regarding reptile euthanasia at Melissa Kaplan's Herp Care Collection
. Check under Page Index - End of Life.
For a more detailed article, check out Penn State Animal Resource Program
This site has specific info about methods/drugs and dosages.