wpDiscuz – Private Comments Addon GPL Overview:
wpDiscuz Private Comments addon is an easy tool to allow commenters to create private comment threads. These threads will be available for website administrators, moderators, and for thread owners.
Addon adds a small button next to the comment submit button to set it as private, also it adds the [Private] button to parent comments to make it private after the comment is submitted.
The buttons to set comments as private can be displayed/hidden for certain user roles in the dashboard. Also, it allows setting certain user roles to moderate private comments.
This feature can be enabled / disabled for certain Comment Forms in case you have many custom comment forms for custom post types.