Maybe the idea could be to have a highlighter function like you find in word processors. Mark a passage with a bright color that sticks with it no matter where it's moved.
Come to think of out there might be a lot of good feature ideas from the general business software world. How about pasting comments like sticky notes? Good for reminders and collaboration.
I know CA covered a lot of the annotation topic in a recent tip-of-the-week (virtual back of the tape box), but some comments might relate closely to a point in time, a specific clip, or a UI detail. These are thing the note fields don't support very well.
Asigning a floating sickly note that would anchor to a specific object might be really useful., especially as routing schemes become more complex.