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? Er... haven’t worked that one out yet. But I'm sure it's there somewhere, though since I tend to work section-by-section I probably don't need it.