Luckily I found this thread because I wanted to make a suggestion to modify the way notifications are displayed!
Currently when I click to view the notifications list, I see something like this...
Many of those notifications are for the same article, and I don't know which belong to that same article. Can you change it so it condenses all those notifications and I see one notification for each comment thread? For example...
PmRd and 5 others have replied to a comment you made in "Firefox for Windows 8 gets new status update."
This makes the most sense because when you click one notification, you'll read the first reply to your comment, and all the other replies below it until the end of the comment thread. If you made a comment somewhere else for that article, it would be another notification. I'd like it this way instead of a single notification per article because I'm not gonna reread all the other comments for that article every time I click a notification for it (and hence I won't re-encounter/find my own comments somewhere else in the comment section for that article). The way it's currently set up, I have to blindly click each notification entry to go through them all.
As for sorting this new setup of notifications, each of these combo notifications would be ordered by the latest comment made. However you'd see the username for the first unread comment in reply to your own comment.
If this isn't very clear, I can see if I can make a Greasemonkey User Script to show what I mean.