I gathered enough courage and went though the 10 pages of this thread :D.
Something that was mentionned at the beginning and that I really miss, is a notification system that will warn you whenever someone posts a reply to a thread (especially a thread you started). I recently implemented such a system in my Ruby on Rails website, it shouldn't be too hard (by the way, what server languages/frameworks are you using for the website ? Just plain PHP ?).
I see there is a "notices" tab section in the user profile which displays a title "Your notifications". These kind of nNotifications could go there ? Or maybe they are supposed to, then it's a bug cause I have nothing there. But then, if you are planning to keep this section for very important notifications only (payment-related notifications for example), then it's probably a bad idea to dilute information there.
Personally, I don't mind being spammed by notifications, so even getting one notification per every answer would be fine.