Replies are not necessarily as good or worse than their parents. A lot of the Sequences on this site might be construed as "replies" to more mainstream statistics, philosophy, or science, and yet I would certainly hope that the Sequence entries would get more upvotes than their parents.
I just found out that a new website feature was implemented 2 days ago. If a comment is voted to -4 or below, it and all replies and downstream comments from it will be hidden from Recent Comments, and further replies in that subthread will incur 5 karma points penalty. The hiding, but not karma penalty, applies retroactively to comments in that subthread posted before the -4 vote.
This seems to be worth a discussion post since most people are probably still voting things to below -3 without knowing the new consequences of doing so.