Theodore Dalyrmple has written an excellent essay in The New English Review on the dynamics of online comments.
I have long been intrigued by the potential value of comments to original stories, and revolted by what passes for discourse in most public media venues. I've toyed around with comment rating and filtering systems to play with the idea that perhaps there are mechanical methods of filtering the sapphires from the gravel, but so far have only come up with a couple of "solid" ideas.
First, if the subject being commented on is serious, the commentor should use his or her real name, and should be verified as a "real" person. I think that, for most people, attaching one's name to a piece helps trigger self-editing.
Secondly, human editing of comments after they're posted, (the old bbs "moderator" function), is critical to creating civilized discourse. Sometimes people lashing out online is simply a way of crying for attention. Once people learn that indeed, people are paying attention to them -- in a good way -- often their behavior adjusts to fit the customs of those around them. Having a moderator "pay attention" and offer helpful hints, then warnings, then censorship/banishment has repeatedly been shown to produce constructive results.
It's worth noting that in the world of online education, the "mentor/proctor" function is seen as one of the best bang-for-the-buck enablers of online instruction.
Third, it's almost a rule that after 100 comments, 95% of all the useful new ideas on a piece have been expressed, and the vast majority of those 100 comments are reactions to the new ideas. This would be a worthy thesis to study I think. The followon would be to create a system that cuts off after 100 (or so) comments, or perhaps 30 main comment threads. After a while the comments just get impossible to wade through.
Finally, as a general practice, it might be a good idea for an author to recap what they heard in the comments (after say, a couple weeks). Sort of a "summary of feedback." This would help close the loop between authors and readers, and help build the relationship between the two.
Just a thought.