This report recommends best practices for development and deployment of modeling, simulation and analysis (MS&A) tools for homeland security applications. The set of recommended practices applicable to any MS&A application includes: modeling practice, software engineering practice/ software reliability, model confidence/ verification, validation and accreditation, standards, interoperability, user friendliness and accessibility, performance, and innovative and unique elements. The recommended practices are discussed with respect to the MS&A application types for DHS that include: analysis and decision support, systems engineering and acquisition, planning and operations, and, training. The practices are also discussed with respect to MS&A application domains relevant to DHS.