Empty folders are not worth nuthin'.
Unless, of course you plan on using them later.
They are good for:
1. Taking up space on your HDD.
2. Making the folder listing larger on your computer.
3. Making the folder listing larger in Windows Explorer.
4. Making you practice how to create empty folders.
5. Making you wonder how they got there later on.
6. Making you practice how to delete them later on.
If you are sure they are empty, they serve no purpose.
Right-click on any empty folder (do not include "Save or Saved" folders for games as saved games will likely be stored there, then click "delete", and voila, empty folder is vamooshed.
;-)