We really need an internal messaging system. I just replied to several comments on my stories which were really questions by people thinking of contributing by leaving another comment. But because I left a comment on my own story, I get the notification and they get nothing, so they will probably never know I responded, and I have no way to flag them down short of making a new thread that say "hey X, here is a response to your question". In this case the person in question is one who is very active on the forums, so I was able to PM them over here, but not everyone on the site uses the forums, and they are separate form the main site.
The old "email to user" was a fairly effective feature. (And thanks much for answering my comment-questions).
I check my emails once in one to three months, but log in to the site at least once a week. So email wouldn't work well. On the other side, if sending a message through the forum, there should be also a notification by email. I just don't know, if it is the standard option. Probably getting an notification on the site and default getting email notifications when receiving a message on the forum should cover all cases.
The email is a standard feature regarding forum messages. I get one every time someone PM's me or responds to a thread I post in. Would be nice to be notified of further comments on thread's I've commented on, though.
Notification on comment replies would be handy, just so long as they can't see your e-mail. I'd rely on forum messages however, if I required a correspondence. My one worry is people having to juggle two sets of messaging systems. "Did you get my message? Did you check your forum messages? Did you check the on-site messages?" The other curiosity that popped into my head is a shoutbox sidebar for people reading the same story, but I'm not convinced that's a good idea.