This paper presents a comparative study of the communication middleware systems suitable for aggregating computational clusters with heterogeneous incompatible SANs into a common Cluster of Clusters (CoC). Being interested mainly in solutions providing the programmer with some single, portable and widely accepted parallel programming model like the Message Passing Interface (MPI), we have narrowed down our choice to a few alternatives: PACXMPI, MPICH-Madeleine III and MPICH-G2. Besides a brief overview of these three alternatives the paper presents our experiences and benchmark results by using two of them: PACX-MPI and MPICH/Madeleine III in the the heterogeneous CoC setup consisting of two subclusters equipped with Myrinet, SCI, and Gigabit Ethernet.