This is, possibly, a crazy idea, but I'm going to float it mostly just to see what happens. Please bear with me and read this through before voting.
Different sites have different community opinions regarding comments. Some are pretty easy-going, others are very strict. Some sites get lots of comments, some get very few.
However, even when the commenting culture is reasonably lax, a large number of comments can easily hide the relevant ones. Flagging and cleaning up after the fact (sometimes automatically, in response to the number and type of flags) is supposed to help with this, but it is mostly reactive.
Suppose instead that each site could choose whether comments should be free once you've reached the reputation limit (the same way they are today), or whether comments should come at a small reputation cost. I'm thinking one rep point per previous, still visible, comment by the same user on the same post.
So the first comment on any question or answer is free. If the same user wants to keep their first comment around, but post another, posting that second comment costs them 1 rep. A third comment with both of the previous ones visible would cost 2 rep, but if they delete the first one, the cost drops to 1 rep (because there's one comment by them visible on the post). The cost starts over from zero if they comment on an answer to that question on which they originally commented, or for that matter when they comment on a different answer. One might even consider upticks on the comment to refund the reputation cost, up to where the total cost for that comment becomes 0 rep, but that has the problem that people very often vote up witty comments that don't add much to the post, the posting of which is exactly what one might hope to discourage with this.
It doesn't even have to be exactly 1 rep per visible comment, but more than that would probably not be reasonable, and fractional rep points would likely complicate a lot of things plenty more than it's worth.
This would hopefully encourage commenters to clean up comments that are no longer necessary, and to restrict commenting to the temporary post-it notes comments are intended to be.
Thoughts on this? I realize it'd take some developer time to actually make this happen, and that there are some things that would need to be worked out before the idea qualifies as an actual spec (for example, what happens when comments are deleted later?), but even those things notwithstanding, is it a good or a horrible idea, and why?