But what if you want to customize what is displayed and what isn't. In order to modify this, you have to change the master page and find the SPHierarchyDataSourceControl node. There are some options that you can choose from documented here: http://msdn.microsoft.com/en-us/library/ms439089.aspx
IncludeDiscussionFolders="false"
ShowDocLibChildren="false"
ShowFolderChildren="false"
ShowListChildren="false"
You can even change the title of what is displayed here. I chose to change the title to Current Projects.
Since the SPHierarchyDataSourceControl also has a "RootWebId" member that can be changed, I can move all archived projects to a new location and create another tree control that pulls from that root. This will give me the ability to display Current and Archived Projects to users.