It is unlikely to find an agile software project not using JIRA, Subversion, CruiseControl, or some other agile productivity suites. One of the most commonly used suites in Microsoft Environment is Team Foundation Server which combines Source Control, Task Planning, Testing, Bug and Issue Tracking, a Build Server, and a Dashboard interface to share documents and ideas in a wiki-like manner.
TFS has an out-of-the-box process template for agile projects, but this template is not fully compliant with Scrum. Since TFS is open for any custom process template, some vendors have provided free templates for Scrum.
The first effort in this area was Scrum for Team System by Conchango. Then a group of VSTS MVPs created a light-weight process template that is easier to install and configure which makes it more appropriate for small projects with small teams.The latest one is eScrum which is provided by Microsoft but as an additional download.
It was also convenient to view the sprint tasks in the form of task board with drag-n-drop capabilities to move tasks between panes. Conchango also had provided Task Board for Team System but it is commercial with one month free trial.
I personally prefer using the TFS integration with MS Office to add tasks in Excel with a running sum of used capacity and then post the tasks to TFS at once. There are many other uses for showing tasks in Excel like conditional formatting of cells to indicate different states, severity, priority and so on.