I don't think it's practical to have the "perfect" personal message index. Perhaps an alternative would be an index of the 20(?) most recent replies directed towards you. This would cover multiple replies in the same topic.
Certainly, not all replies call for replies in return. Please DON'T start replying just to clear the "replies waiting" list.
I receive the e-mail notifications for replies to both Adminnemooseus and minnemooseus. If you are not already doing such, you may wish to try it out - Go to your profile page to set it up. That way you have a complete (and as lasting as you wish) index to all replies to you.
Maybe it would be nice to also have e-mail notification of your own postings. That way you would have an index of those also.
Adminnemooseus