This paper proposes a new general method for supporting production systems design within the context of Multi-objective Simulation Optimisation. Under this framework, different Production Control Mechanisms can be compared based on their optimal settings, which will be illustrated with a pedagogical simple flow line as well as an engines assembly line in automotive industry. Results from these case studies have provided significant insight into the importance of applying MOSO for Multi-Criteria Decision Making in general production systems design. At the same time, it also outlines the concept of applying significant dominance to handle uncertainty from stochastic simulation output, which has been implemented into a Web-based DES system called FACTS Analyser, specifically designed for conceptual factory design, analysis and optimisation.