Personally, i don't use sending mails by forum at all. If You have thread subscribed, and you log in, then proceed to Control Panel, first thing You see is list of Your subscribed threads with new posts (don't confuse it with "Subscribed Threads" list, that show every subscribed thread, no matter of new posts being posted or not). You also got Your PM's there - if any new - so, basically, it's Your custom view for any new content that You might feel interested in.

If You add to this "Active Topics" panel, that could be enhanced to allow setting up categories You're interested in (or tags), I think everything needed to properly manage Your threads of interest should be available.

/Estel