I’ve published on codeplex a small command-line tool to administer work item queries: wiqadmin.
This tools, compatible with TFS 2008 and TFS 2010, supports the following commands:
- List queries.
- Export a query.
- Import a query.
- Rename (and/or move under TFS 2010) a query.
- Delete a query (or a folder under TFS 2010).
The TFS 2010 version supports folders 
Carpe Diem.