Initially when I launched this beta program you needed to end you email replies with
This is no longer the case. Simply reply to the email, above the original quoted message, and send the email.
As it is a trickier problem to solve than meets they eye there may be a few quirks for some email clients, but so far it is working.
I have also updated the plugin to improve the formatting, please update.
Soon I will be providing support for transactional email services like Mandrill which you won't be able to use currently due to header restrictions. It is not bad idea to use these as although this plugin should not add much overhead, more people using notifications will, as will larger user bases.
grep is your friend.