I'm not sure how easy this is to implement, but....
I've noticed that when I get on after a weekend off the Newest Nodes page is heavily clogged. (I can only imagine what happened with ZZamboni, who just returned from a vacation).
I could just clear the list, but I like to go through and read the threads for good messages to vote up and learn from.
So here's my thought:
Why not only list Notes/Replies to threads that are NOT listed as Newest Nodes?
Of course, to be perfect it would have to know the ancestor node, which it probably doesn't, otherwise we'd have links to the thread-starting node. But a simple Regexp should match most of situations.
That's my 30 second version to match the name of the ancestor node in $2. Doubtless a better one could be worked up with a little effort.