Let me start of by saying that this article is all about sorting comments by color in Acrobat 9. You may ask, "Why are you writing about features in old software? Acrobat X has been out for over a year now." Well, sadly, Sort Comments by Color (my favorite Acrobat feature) was removed in Acrobat X. So I still use the old software. But I digress.
Sort Comments by Color is at the heart of my production workflow. I have a dozen or so colors that I use to color-code pertinent parts of my documents. Each color represents a similar type of information. So when I'm working an a project, I'll start with the pink comments, then go the gray comments, then to magenta, and so on down the line. The Sort Comments by Color feature allows me to group all the similar information together so that I work on it more easily.
So, once my comments are sorted by color, there is another secondary level of sorting that Acrobat uses. It doesn't sort as you think it might. It sorts not by where the comments fall in order of creation, nor where they fall in the page sequence (as you'd think they might), but rather, Acrobat sorts them based on the Y coordinates. Like so:
In the example above, I have two purple comments: the first is on page 1 at the bottom of the page, and the second is on page 2, near the top of the page. In this example, the comment on the second page will appear at the top of the list when sorted by color.
If you'd like to read more about Sorting Comments by Color: check out my other article on the topic: Acrobat Rectangle Tool: Why Do You Disappoint Me So?
Edit 10-9-14: I recently found a useful add-on for Acrobat X and XI. It allows you to filter comments by color. While it doesn't have all the same functionality as Sort Comments by Color in Acrobat 9, it may be a good choice for those that use color-coded comments and do not have access to Acrobat 9. Here is the script: Acrobat -- Filter Comments By Color
Edit 9-25-15: Please check out my latest article: Sort Comments by Color... In Acrobat DC!
Edit 7-12-16: I'm happy to report that when Adobe finally restored "Sort Comments by Color" back to Acrobat DC, they fixed the secondary sorting issue. So now, when comments are sorted by color, they are listed in order by page, then by Y-coordinate.