The comment interface on HN is embarrassingly bad for large threads. I've been meaning to do a separate writeup about this, but the gist of it is that the epitome of a great interface for managing threaded discussions are some Usenet news readers, which have relatively advanced features like kill files, filters, sorting, collapsible threads, user-controllable thread marking through color codes and tags, actions that can be taken based on the contents of the title and/or body, etc..
Even ordinary web forums are atrociously primitive in comparison, and HN comments are even more primitive than that. The simplicity might arguably be an advantage for very short threads. But for long threads the lack of features can be a nightmare.
At the very least I'd like the HN interface to flag which comments are new since the last time I refreshed the page. That way I don't have to manually reread many dozens of comments in the longer threads while trying to remember which comments I've already read.. and do this over and over and over again as I reload the page.
If you use Chrome there's an extension for that. I don't remember what it's called or if it works on other browsers but I'll find the name and update this when I get back to a real computer.
I don't think it works on different browsers and it can get annoying when you use multiple machines because the read comments don't transfer, but otherwise it is a very nice tool.
Maybe limit the maximum reply depth? (to 4 or something well low)?