A note in the header of the reply as to whether the reply was flagged would keep the clutter down.

Very good idea. Perhaps in the form of a link optionally bringing to an "extended" text. Or a combination of the two. I had originally thought of a node because AIUI under the Everything2 engine everything is a node, after all. Of course a node to be rendered from the UI POV in such a light manner to be like a one comment line... no links, no bells and whistles... and perhaps in the footer rather than in the header. (I would make it look like part of the node it applies to, with a color that would stick out, but in small enough text. Of course it would all be depend on suitable css settings.)

The point being, as with the other ongoing discussion I mentioned, that PM is very KISS and that's one of its strenght so any "improvement" to the current and working mechanisms, even before crashing on the wall of actual and possible implementation difficulties should be thought of as making sure about not getting in the way of that...