I recently started reading up on the Django framework. The creators of Django, Adrian Holovaty and Jacob Kaplan-Moss, recently finished publishing a book that describes Django and how best to use it. They published both an online version of their book as well as a print version.
The online version has a UI innovation that I loved: the ability to leave comments inline with the text. I often find it quite distracting to scroll between comments and the main text when reading some online publication formats. And in this case, a wiki was not an appropriate format in which to publish a book.
Instead, the site allows users to click on the left side bar, which changes to a slightly darker shade of green when you hover over it. Click on the sidebar and a comment box pops up. If comments had already been left, then you see a little callout indicating the number of comments that have been left around a particular paragraph. I believe the authors used this facility extensively while their book was in “beta” to get feedback and errata from users.
The AJAX pop-up lets you read others comments as well as post new comments:
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