When there are many comments to a question and they get to be almost a mini-thread it might help to have an enumeration system. So you could respond to comment say 15 when you are at say 42. Not a major issue though as usually there are few comments.
The comment section has never been intended for extended discussions. If you find yourself in a situation where you need complicated systems to keep track of the discussion, you should have it in chat instead. (You can even create chatrooms to address a specific question/post!) (In fact, for long comment threads the software will nag you to "let us continue this discussion in chat".)
For all else Martin's suggestion should be more than sufficient.