Rename-It! is a Windows software to safely rename of thousands of files and folders at once via RegEx and all kind of other renaming filters. See the wiki section for more details.
Download latest version from http://download.beroux.com/renameit-4-dev-setup.exe
Thanks to Giuseppe Pischedda there is now a 64-bit working shell extension, you can see his website at http://www.software-on-demand-ita.com/Downloads/RenameIt
The project's directory stucture follows the Java BluePrints project conventions (http://java.sun.com/blueprints/code/projectconventions.html).
Each folder should contain a README.txt explaining what should be in that folder. Most names are self-explanatory.