From the Scoring/Criteria section of the website:
"The ranking scheme, developed with the help of a scholar from Yale's School of Forestry and Environmental Studies, was intended as a tool for identifying, for the purpose of spotlighting, those cities that are taking the lead in addressing the major environmental challenges of our time, from global warming to clean air and water."
Seattle, WA currently tops the list, with many California cities close behind. The useful grid format of the scoring reveals the strengths of each city in factors such as transit, green building, and water quality and conservation.