I am looking for online exhibit software that provides collaborative annotation for texts and the ability to compare different editions of a text to identify differences (e.g. Juxta). Does Omeka have plug-ins that offer these features? I've looked at ImageAnnotator and Google Docs viewer, but they are not quite what I need.
Not exactly that, but there is a plugin in testing stages for the Scripto Tool that will allow you to transcribe a document or any item and have that available together with the original file. Read more about Scripto: http://scripto.org/
This could offer a similar comparative environment that you are seeking.
Alternatively, if you wish to use something like Juxta we would encourage you to investigate building a plugin that allow it to work with Omeka items.