One FCRN network member has kindly responded to the request for info on more footprinting tools.
She highlights the Fieldprint calculator (on-farm only) developed by The Keystone Alliance for Sustainable Agriculture. The tool calculates not only carbon but also incorporates soil and water use indicators. Reference values are included to enable the user to establish how his/her farm compares, but as the tool was developed in the US that aspect of the tool may not apply in other regions.
Another tool she highlights is more of a carbon forecasting tool. It was developed by the FAO to estimate the potential impact of agriculture and forestry projects before they happen, i.e. at the planning stages. More here.