Like for example lets say a new user ask a RMT. I comment on it to give a suggestion. Some later comments on it talking to me. I have no idea if someone commented back unless i go back and check the question everytime it gets a comment(Which would be pretty annoying). Or lets say you comment on a question asking the user who answer about some information. You never know if they ever commented back unless you check. So what i suggest is that when somebody wants to reply to you they can type @Unrecognizable before typing a message it would alert the user saying "You just got a new comment" and if they are not online it would pop up when they log in. Sort of like how youtube tells you when someone reply to your comment on a video.
Dr.Flame answers a question about how to get the stones on B/W saying that you can find them in the duskclouds inside of caves. I have a question about the stones so i comment asking him about it. If he replies with "@Unrecognizable" then his comment i would get a little message at the bottom of my screen telling me i got a reply to my comment.