There is a folder in the System Filesystem called Loaders. It is where various things are registered that apply to specific DataObject types. For example, there is a folder Loaders/text/x-java that contains things that pertain to Java files (notice that the path is a MIME type). It has an Actions subfolder where you can add actions to the popup menu for Java files.

You may not think of a folder as being a file type, but to NetBeans it is. There is a subfolder Loaders/folder/any/Actions which contains actions that should appear in the popup menu for folders. Just add your action in your layer file to that folder, i.e.

<filesystem>
  <folder name="Loaders">
      <folder name="folder">
          <folder name="any">
            <folder name="Actions">
               <file name="com-foo-module-MyAction.instance"/>
          </folder>
        </folder>
      </folder>
    </folder>
</filesystem>

Source: NetBeans FAQ