My experience with CO2
I have never had to put down a reptile yet, but at my work we have a hamster/rat/gerbil etc breeding business. For the first couple of months the only times we had to put anything down were babies that were obviously not going to make it past one day. I tried to do some research on freezing animals but it is all conflicting about whether it is painful or not. Anyway, after looking at the american veterinary medicine association's euthanasia report
www.avma.org/resources/euthanasia.pdf we decided CO2 would be a better option.
So we went to our local sportsmart and bought a small canister of CO2 for about $25 normally intended for paintguns. The refills are about $3 but we have had the canister for months now and it is still running strong, and we use it frequently for feeders. We now CO2 our feeder mice and rats, and any other animals seriously in need of euthanasia. What we do is grab a small plastic bag, the type used to bag up fish for customers, put the animal in it, take out most of the air in the bag, wrap the opening of the baggie around the neck of the CO2 canister, and press the pin down to fill the bag up with CO2. Then the bag is tied shut and the mammals will become unconscious within 30 seconds usually. The animals do a 10 second struggle to get out since they arn't getting oxygen, then become unconscious. Once unconscious they do a gasping action which is a little sad to watch, but they are not conscious anymore so they no longer care, and by the time that I manage to tie the bag shut they are usually dead.
So relating this to reptiles, I still think it would work. The baggie method makes it so that the animal stays immersed in CO2 for as long as it takes. Small amounts of CO2 will make the animal light headed, then they go into an anesthetized state, then become unconscious, then finally dead. So even if it takes a while the reptile will not be in pain unlike, as some speculate, freezing would be.
I know that if I need to put down a leopard gecko at some point, I will use CO2.