In most project portfolio selection (PPS) situations, the presence of multiple attributes and decision-maker preference is inevitable. As Multi-criteria Decision Analysis (MCDA) methods provide a framework well-suited to deal with these challenges in PPS problems, the use of MCDA methods in real-life PPS problems has increased in recent years. This paper provides a comprehensive literature review of the use of different MCDA methods and their individual or combined utilization with other modeling techniques to support PPS problems. First, we summarize how MCDA methods are used in different modeling approaches. Second, we examine the mathematical models that are generally used to combine MCDA with mathematical programming techniques to solve PPS problems with resource constraints. Third, we present the drawbacks of combined utilization and discuss recent advances. Finally, we provide a decision tree based guideline to assist researchers and practitioners in the use of MCDA methods in a specific PPS context and propose some future research directions.