We currently are using both Visual Source Safe and Team Foundation Server at work (VSS for old projects, TFS for current or new projects).
We have always used Labels
[due to the complexity of TFS-style labels this is a quite difficult problem when applied to folders; based on a comment above I'm going to assume searching for labels on a file is sufficient]
Unfortunately this is one of the very few edge cases of the TFS client API that is not exposed anywhere in tf.exe or VS2008. You'll have to call the API directly. Please see http://msdn.microsoft.com/en-us/library/bb138967.aspx - the "versionFilterItem" parameter does what you're looking for.