This paper discusses specific models and analyses to select the best cogeneration planning solution in the presence of uncertainties on a long-term time scale, completing the approach formulated in the companion paper (Part I). The most convenient solutions are identified among a pre-defined set of planning alternatives according to decision theory-based criteria, upon definition of weighted scenarios and by using the exceeding probabilities of suitable economic indicators as decision variables. Application of the criteria to a real energy system with various technological alternatives operated under different control strategies is illustrated and discussed. The results obtained show that using the Net Present Cost indicator it is always possible to apply the decision theory concepts to select the best planning alternative. Other economic indicators like Discounted Payback Period and Internal Rate of Return exhibit possible application limits for cogeneration planning within the decision theory framework. (C) 2010 Elsevier Ltd. All rights reserved.