Utopia Docs is a desktop app (PDF reader) + web service that allows users to annotate PDFs in a localized (anchored), conversational format. Annotations are universally visible: if another user opens the same PDF, they’ll see other users’ annotations.

http://getutopia.com/

Stack Overflow

Upvoting/downvoting of questions/answers/comments, credit accumulation, new capabilities as credit is accumulated (e.g., can only upvote comments after some number of points have been gained).

Mismatch between length of questions & the long-form articles we want to be able to handle.

http://stackoverflow.com/

Commentpress

Fine-grained commenting theme for WordPress, so that conversations can happen on paragraphs. Big advantage over Utopia: in the browser; in WordPress and therefore more hackable.

http://www.futureofthebook.org/commentpress/

Annotum

WordPress theme for “journal” publication/review used for PLoS Currents

http://annotum.org/

http://currents.plos.org/

PLoS Hubs

“Portal” platform, currently only one example.

http://hubs.plos.org

Thoughts/mashups

• Pull Utopia Docs/other annotations could into a Stack Overflow or other-like service via an API?
• WordPress-based solution using Annotum/CommentPress/ratings plugin, etc., etc.
• Some other content management system/framework (Drupal etc.)