1. A method of supply chain facility performance analysis, the method comprising: maintaining, via a computer processor, supply chain facility configuration information for a plurality of supply chain facilities, the plurality of supply chain facilities classified by supply chain facility organization type; identifying, via the computer processor, variables that are attributed to performance of the supply chain facilities, the variables for each of the plurality of supply chain facilities vary according to the supply chain facility organization type; collecting, via the computer processor, data corresponding to one or more of the variables for selected supply chain facilities in the plurality of supply chain facilities; performing, via the computer processor, performance analysis for the selected supply chain facilities using the data as input, the performance analysis including executing a data envelope analysis (DEA) based three-stage performance analysis model, executing a statistical analysis and executing a sensitivity analysis; and outputting, via the computer processor, the results of the performance analysis to at least one of a display screen and a storage device, the results including a performance ranking of the selected supply chain facilities, the prescriptions for performance improvement, and results of the correlation analysis and the sensitivity analysis; wherein executing the data envelope analysis (DEA) based three-stage performance analysis model comprises: performing a first stage DEA analysis on only the data that is attributable to discretionary variables and deriving efficiency scores resulting from the first stage DEA analysis; performing a second stage linear programming optimization and discovering any excesses and shortages that provide prescriptions for performance improvement based on the second stage linear programming optimization; and regressing the data attributable to non-discretionary variables onto the efficiency scores and distinguishing inefficiencies attributable to the discretionary variables from inefficiencies attributable to the non-discretionary variables.