Check out your Personal Nodelet, which stores any node you want as part of your PM user data. You may need to enable it in your User Settings. Currently, there's no way of indicating when a new message is posted to a thread, but that seems to be a highly requested feature for PM.

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Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain