In the Planning Manual, Chapter 10 provides criteria and approaches. See pages 205-216 of the manual.
Additional references may be found on the Institute for Water Resources publication page under Environmental Evaluation, http://www.wrsc.usace.army.mil/iwr/Products/reports/reports.htm#EE. See especially reports that address cost-effectiveness, incremental cost analysis, and trade-off analysis.
Software called "IWR-Plan" is available through http://www.wrsc.usace.army.mil/iwr/Oldnews/IWRplan.htm. "IWR-PLAN makes it easy to do sophisticated cost-effectiveness and incremental-cost analysis. Incremental-cost analysis is an alternative to benefit-cost analysis used when the primary benefits of alternative plans are not measured in dollars. For example, Corps planners can use IWR-PLAN to compare the incremental environmental outputs or benefits gained with successively more expensive ecosystem restoration plans. IWR-PLAN also helps formulate compound alternatives from simple user-provided measures. In a typical ecosystem restoration study, there are many possible measures which could be implemented independently or in various combinations. Ideally, a planner would like to see the costs and environmental benefits of each combination. IWR-PLAN 3.0 makes it easy to form these combinations and then evaluate their costs and benefits."
It should be recognized that for each alternative that provides a "cost" to IWR-PLAN, there must be a corresponding environmental analysis to obtain a discrete output or benefit. Often such analyses are time-consuming and complicated. However, software called "EXHEP" and "EXHGM" has been developed in the Windows operating system to automate applications of the Habitat Evaluation Procedures and the Hydrogeomorphic Wetland Assessment Approach. Results of EXHEP or EXHGM can be exported to IWR-PLAN to aid in comparing alternatives. EXHEP and EXHGM can import and export data from Microsoft-compatible software packages. Output generated can be directly transferred to standard spreadsheet and word processing software packages. Contact Kelly Burks-Copes at Kelly.A.Burks-Copes@erdc.usace.army.mil for information on obtaining EXHEP and EXHGM.