I am using WinMerge build 126.96.36.199
It would be nice if WinMerge could add support for the additional version control systems, such as MS Team System.
Perhaps the answer would be to add support for "arbitrary" version control systems, by adding the ability to configure a command-line for performing actions such as checkout.
For MS Team System, Microsoft have a "Microsoft Visual Studio 2005 Team Foundation Power Toy" available that is a collection of command-line tools performs all the various version control functions. (see http://msdn2.microsoft.com/en-us/vstudio/aa718351.aspx\)