Users can choose to :Receive Comment Reply Notification Only: or :Receive Notification For All New Comments: or :Not Receive Any Notifications:
UPDATE: Users now have three options to choose from:
Do Not Send Email Notifications.
Send Email Notification ONLY If Someone Replies To My Comment(s).
Send Email Notification Whenever A New Comment Is Posted.
If a user chooses the second option, then email notification will only be sent to him when someone reply to his/her comment by clicking on Reply button below the comment.
You can find more information here: http://elance360.com/wordpress-plugin/
For this plugin to work, you will need to enable Threaded/Nested comments option.
:Send email only on Reply to My Comment: is a Modified version of this plugin :Subscribe To Comments Reloaded: