This paper presents an algorithm to compare traditional and innovative energy systems for maritime applications, adopting a multi-criteria method. The algorithm includes a large and updated database of market solutions. Two case studies are investigated: (i) a sailing yacht (ii) and a large-size cruise ship. For case (i), Fuel Cells represent a competitive solution, in particular considering navigation in emission control areas; the installation of electrical batteries is also evaluated. For case study (ii) Internal Combustion Engines are the best solution: the evaluation of alternative fuels (LNG, ammonia, methanol) is performed, also in dual-fuel configuration.