With the advent of heterogeneous computing systems consisting of multi-core CPUs and many-core GPUs, robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated runnings costs and even carbon emissions. We give a case study for these metrics applied to BUDE, a molecular mechanics-based docking application that has been ported to OpenCL at the University of Bristol.