Can you add a flag to the posts themselves that indicates whether they are new or not? It can even be small and subtle like the difference between
(new) and
(old) that is used at 3rdedition.org. I know that having those flags makes it just that little bit easier to keep up with threads you are tracking (i.e. it indicates where you need to resume reading).
Along similar lines, it would be nice if the Sticky Topic, Announcements, Closed Topic, and Moved Topic symbols had grayscale versions for old ones like the normal Topic and Poll markers do.