One of the important concepts in Team Foundation Server are Process Templates. Process Templates allows you to easily customize and adapt Team Foundation Server to integrate a development/project management methodology of your choice. Out-of-the-box you have 2 options available:
Recently Microsoft added a third template focussing on Scrum.
Of course they are also a lot of other (free) templates available. But which one is best suited to your needs?
Crispin Parker (one of the guys working on the Scrum for Team System template), created a feature comparison between the Microsoft templates and the Scrum for Team System template. So if you are using Scrum and want to integrate with TFS, check out this post.