The ideal annotation tool would allow notes to be associated with highlights. It would have the option to specify what is included with each highlight or note, including: a citekey, a hyperlink back to the source, and a tag tool for note tags.
Beyond keeping my PDFs together, I want to be able to extract important information from them. I don’t just want to visually tag different parts of the PDF, but I want to be able to actively work with those bits of information. The next key advancement is to add semantic information to the text (or image) snippets.