As many of you know, I have discussed this problem before. I have not found a general solution yet but I wanted to highlight one other problem that has manifested recently. When I get comments back from my supervisors, I have noticed that they either reference their comments by section number or page. Those that have worked with LaTeX know that the section numbering is automatically generated and you do not know the page number of something until you have compiled it to its final form. In this case, I generally lean on EMACS' search function to find where I should change something.
I am now very near the end of my PhD so it is less of a problem than before. However, I have a friend in Education to whom I taught LaTeX but she had to give it up because all of her professors use the comment features of Word to give feedback. I think that if LaTeX or PDF had an easy (and non-expensive) method for obtaining feedback, the Humanities might be more willing to give up its Word habit.
This causes me to wonder how people in Computer Science and Mathematics make comments on a LaTeX produced paper? Hopefully, I will come up with some kind of solution when I have more time to think about it.