Chapter 9 of the Planning Manual addresses evaluation of alternative plans, using criteria of completeness, effectiveness, efficiency, and acceptability. See pages 181-203 of the manual.
This step can be thought of as impact assessment if the consequences of the alternatives are negative, and a huge body of literature and practice exists for that topic. If the consequences are thought to be positive, i.e., in restoration work, the same tools can often be applied. Problems have become opportunities, losses have become gains.
In either case, some quantification is necessary. The section of EMRIS on Decision Support Tools contains some information on Habitat Evaluation, which has quantification as its basis. 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
Significance is relevant at this step. Significant resources should be highlighted in the assessment of alternatives. The significance of planned outputs and effects should be determined. Criteria for judging an output or effect to be significant include the extent of the change, the amount of controversy or public interest, the context of the project or action (i.e., what else is affected), and the degree of certainty in the outcome. The degree of change can be considered in extent, magnitude, intensity, and/or duration of the effect.