As previously mentioned, comments now have a 'notify flag'. When you leave a comment now, there is a tickbox which you can tick to receive notifications when new comments are added. The granularity is very broad though, it will notify you if there's any comments added to the entry, not just the reply you've made.
I've also implemented comment replies, which will display replies underneath the comment to which it was a reply. I'm not overly happy with the layout at the moment, but it's the best I've got and I can't really put my finger on what I don't like anyway! If you've had a Patron diary re-imported and that diary had comment replies (because WordPress supported comment replies, or 'nested comments') then these should now be displayed correctly, as I have implemented the system with that in mind.
I've also implemented a requirement that anyone leaving a comment must have set a Username in their profile before they can leave the comment. This stops the comments section being filled with comments from: <blank>.
I think that's about it for now. Let me know what you think or if you find problems!
EDIT: Oh, comments now show the oldest comment first because trying to follow a thread of comments is really unintuitive if the newest comment is shown first 😀