Xilinx has recently published an app note detailing how to configure Subversion with SimDiff and SimMerge for team-based development of Simulink models.
From the app note:
"This application note provides an overview on how to perform source version control and team-based design using the System Generator tool. These tasks can be accomplished using the version control features native to the MATLAB®Simulink® software environment, or with an external source control system. While this application note focuses on Subversion, a well-known, free, open-source control system, other version control software such as CVS, MS Source Safe, and Clear Case can also be used—depending on the design environment. This application note also demonstrates how to graphically compare and merge model-based designs using the SimDiff and SimMerge external software packages from Ensoft."