In a word, comments. I've always wanted to be able to make comments easily throughout a manuscript and never found a great way to do. General word processors usually offer to do them in the margin, and then expand the page size to include them.

Not Scrivener 2.
<p style="text-align: center;"><img class="size-full wp-image-7959 aligncenter" title="Screen shot 2011-04-05 at 08.00.24" src="http://davidhewson.com/wp-content/uploads/2011/04/Screen-shot-2011-04-05-at-08.00.24.png" alt="" width="353" height="59" /></p>
Put your cursor in the text somewhere and hit the comment icon (or Command-Shift-*). You can then put a comment directly into that position. But you see it in the hideable Inspector sidebar, where version data, notes, snapshots, keywords and references also reside.

<img class="aligncenter size-full wp-image-7961" title="Screen shot 2011-04-05 at 08.00.00" src="http://davidhewson.com/wp-content/uploads/2011/04/Screen-shot-2011-04-05-at-08.00.00.png" alt="" width="288" height="86" />

So it's there when you need it and somehow a lot less distracting than a comment placed in the margin of the actual document.

Want to see all the notes for a section of different scenes? Select the enclosing folder. Want to see all the notes for the manuscript