For a long time the comment system here has been lacking, and while the following changes by no means make it perfect, I believe they will help those actively posting and replying to comments. The first change you will notice is inline replies. Now when you click the "reply" button the reply box opens directly below - this should make it much easier to know what you are replying to.
The second change is opt-in, which basically emails you whenever someone replies to a comment you have posted. To turn this on, edit your userprofile and check the following box:
Other changes I am considering include notification when people post a comment in a profile you control (i.e. if you run a mod and someone comments in there, you will be emailed, same for news posts and media). However I am concerned that would result in too many emails and so have not done it at this point. Also considering adding the ability for Facebook / Twitter users to post comments easily and a way to view your comment history in your user profile.