Email notifications should be sent to commenters when replies (or questions) are posted to their comments. Otherwise comments which need followup will have loose ends and the question might not get an approved answer (question gets abandoned prematurely).
If this is even considered, it should only be after a long period of account inactivity. I'll throw out one week as a starting point. It should also be disable-able on your user preferences page. I don't need dozens of notification emails from a site I visit every day. :)