If you’ve ever left a comment-reply to users who’ve left comments on your site - you’ll get a email notification the same as you do for every commenter. This can prevented however.
Go to lib/MT/App/Comments.pm in your MT folder and find the line that reads:
This is on line 152 if you’re using MT 2.64. Change it to:
MT::Mail->send(\%head, $body) unless $author->email eq $comment->email;
And you’re done. However, if you’re using Jay Allens MT Blacklist plug in, you’ll need to change the code in the Blacklist.pm file instead. ScriptyGoddess shows you how.