Many third-party vendors have designed process templates for Team System. Here is a breakdown of the resources currently at your disposal:
SCRUM - Conchango has developed a fully featured Scrum template for Team System. You can download the template for free at http://scrumforteamsystem.com.
Essential Unified Process - Ivar Jacobson, inventor of the Rational Unified Process has devised a lightweight, Agile process for Team System called the Essential Unified Process. You can learn more about this process and the process template at ivarjacobson.com.
Feature Driven Development - Cognizant is working on a feature-driven development process template for Team System. You can learn more about it by downloading the following white paper: http://download.microsoft.com/download/1/b/7//Cognizant%20FDD%20Implementation%20with%20VSTS.pdf.
It is also important to note that Microsoft is continuously updating and improving the CMMI and Agile versions of MSF. They are also working on a Sarbanes-Oxley (SOX) compliant version of MSF. If you use systems such as Six-Sigma or feature-driven development, you can customize a template to meet your needs. Some companies may require special customized process templates for ITIL or the Canadian CICA 5900 requirements.
Rarely will a company adopt a process in its entirety. You have to modify and tailor any process to fit your needs. For example, you may have roles that don't quite fit those available by default in the MSF for Agile Software Development and MSF for CMMI Process Improvement process templates. Another possibility is that you have to modify the work items to be able to capture and store information that may be important to a company from a business perspective.