Well, from what I can tell, there is no difference in quality between the 'whack a rat' method and CO2.
Initially, I had been concerned that CO2 euthanasia used for feeders could be unhealthy for the animals consuming them. Off the top of my head, I think the way CO2 kills is by not only preventing the proper amount of O2 into the tissues, but also by preventing cells from filtering out toxic by-products of normal metabolism. Like I said, this is all off the top of my head, and as I write it, it isn't sounding quite right. Anyhow, my concern was that the rodent killed by CO2 might have a bad effect on the snake that would consume it.
To back this up, about a year ago a friend of mine notified me that the Ball Python I had given her in 2003 as a 5-year-old had died. He had been the picture of health before that, and she wasn't new to snake keeping. She suspected the culprit to have been a "bad rat," since he had eaten not too long before his death. We're still baffled by that one. Ball Pythons should live well into their 20's or better without any fuss.
Anyhow, I started asking my professor in Meat Science about any meat quality effects from CO2 euthanasia. I was actually shocked to find out that this method had in fact been used in many places to euthanize livestock meant for human consumption. With that being the case, there are several studies available about the effects of this euthanasia method on meat quality... which I have been too stinkin' busy to look up and read. 
Apparently the only reason this method fell out of favor with meat packing plants is that it is not efficient enough for the vast numbers of animals that get processed on a daily basis.
What I definitely learned from my Meat Science course though is that the amount of time between the death of the animal and the tissues being cooled to around 40 degrees Fahrenheit is the biggest factor affecting overall quality (that is of course aside from the initial health of the animal in question before euthanasia).
How I apply that to what I do with my snakes is just to make sure that I pay very close attention to how long I leave any pre-killed prey sit with a snake before I freeze it if the snake isn't going to eat it - if I can, I set the limit at around 20 minutes. Also, I pay a lot of attention to how long I spend thawing prey. There have been some very interesting threads in the Ball Python forum on thawing methods... and while I don't think my thawing method is the best out there, I know it is better than some others. I put the prey item in a sealed zip top bag and submerge the bag in hot tap water for about 20 minutes at a time, which does vary with the size of the prey. This seems to work pretty well, and the thawed prey definitely smells better when I do this than when I get tied up doing something else and forget I've left something thawing... grrr!
Either way, if you can minimize the amount of time that the dead thing sits around at warm temperatures, you can maximize its nutritive value to what you are trying to feed. 
~Rebecca
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0.1 Dumeril's Boa '04 (Courtney)
1.2 Ball Pythons
[1.0 '05 Orange Hypo (Specter)]
[0.1 '05 Het Orange Hypo (Sylvia)]
[0.1 '03 Normal (Sue)]
0.2 American Pit Bull Terriers (40lb darling lap dogs:Brandy&Mara)
