I think John is exactly right about this. I gave a talk[1] about this back in September, trying to argue that, especially with climate science, where methodologies are evolving constantly, the key assurance to quality is transparency. My company, Brighter Planet[2], does real-time carbon calculations via web services, so this is an ongoing concern for us. The steps we've taken so far:
* We release all of our carbon models[3] as open-source code under the AGPL.
* We provide custom-generated methodology documentation like this [4] for every one of our calculations.
* We're using Rocco[5] to do literate-style documentation of our methodologies, with specific focus on compliance with standard carbon accounting protocols.
The sad truth is that if you enter the same input data into each of the hundreds of carbon calculation software packages available now, you're going to get a different answer each time. To be fair, all science is uncertain, so this is somewhat to be expected. But with transparency--especially documentation and open-source code--at least we'll know why.