The standard for carbon footprinting is ISO 14064-1. It is more or less a summary of the WBCSD/GHG Protocol. The problem with this standard is that it does not lead to standardized, comparable carbon footprints. This is because the standard leaves important choices open to the user. One of them is the way the user selects emission sources to report from - the organizational boundaries. The other is the way scope 3 [other indirect] emissions are reported - the operational boundaries. Organizational boundaries: You can choose between a "control approach" and "equity share". In the control approach you report 100% of the emissions from sources over which you have financial or operation control. In the equity approach you only report the your portion of the facility - if you own 20%, you report 20%. In the equity approach you also report zero emissions for leased assets, since you don't own them. Imagine a bank with a leased office and leased cars. Their emissions will be zero in an equity share approach, whereas they would be fully reported in an operational control approach. Operational boundaries: You can choose to not report scope 3 emissions at all. Most of the companies that do report scope 3 emissions limit the categories to commuting and business travel. Normally, mapping scope 3 emissions leads to [1] a lot of work collecting data with large associated uncertainties and [2] dwarfing of your scope 1 and 2 emissions. For example, the use of your Apple computer represents more than half of the greenhouse gases that can be associated with Apple. What is being done about this? The carbon disclosure project [www.cdproject.net] is proposing that companies report using the financial control approach. ISO is working on a standard that gives further guidance to the application of the standard [ISO 14069, draft]. The WBCSD/WRI is working on tools for better assessment of scope 3 emissions [www.ghgprotocol.org]. For the time being you will have to take a very good look at the details of the carbon footprint of an organization before you start comparing.
