RED searches and deletes empty directories recursively below a given start folder and shows the result in a well arranged tree. Further you can create some custom rules for keeping and deleting folders. Empty files in directories can also be ignored. Just try RED to see the other features - no registry keys or system files will be touched.

Disclaimer
Some applications may require temporary directories that are empty. It could be possible that some applications stop working if such a temporary folder gets deleted.
System Requirements
Microsoft .NET Framework 2.0
(The installer should check if you have installed the .NET Framework 2.0 and will install it if not)

Download Remove Empty Directories v2.1