Came across A.nnotate.com whilst reading the comments here. In A.nnotate.com you can
search and browse the text, tags and notes
any part of the text can be annotated or even regions of an image
In the tools section, you can get an index of all the tags and you can also get a text file with the notes taken.
Unfortunately it is not free so I have only played with the example files and I am not sure my links will work but I thought it could be really good tool to integrate into BHL, GoogleBooks and Mendeley for example as it has the ability to pull up text sections across multiple documents using searches and tags so collaborators can mark-up pdfs and share their tags and notes.