Windows Mobile 6 provides excellent compatibility with Windows Mobile 5.0 applications. Windows Mobile 5.0 compatibility was an explicit goal of Windows Mobile 6 and has been heavily tested throughout the Windows Mobile 6 development process. The overwhelming majority of Windows Mobile 5.0 applications will run on Windows Mobile 6 devices without modification. The only caveat is that compatibility is conditional on the applications use of supported APIs. As you might suspect, Windows Mobile 5.0 applications that use undocumented or unsupported APIs may experience application compatibility issues not experienced by those applications that use supported APIs.
We've just published an article to MSDN that outlines the new capabilities for Developers in Windows Mobile 6.
You can check it out HERE