I really like the way Mendeley handles notes, specifically highlighting / annotating PDFs. Do you know of any alternatives that include this? I was planning on writing my own at some point but it might be a bit ambitious.
I chose it a few months ago over mendeley because it allowed me to search in the PDF annotations, which isn't possible with mendeley. I recall mendeley could search notes added to a PDF file (one text area for the whole file), but not within sticky notes attached to specific pages, so it was impossible to search the annotations I made and also have those annotations appear on the relevant part of the PDF.
The other thing I like about qiqqa is that it allows us to have a shared library on our local server, instead of having to send all our data to the cloud.
Both are great desktop tools for full text search across many PDF files, even those that need OCR. Before I was using google desktop for this function, and qiqqa is definitely a step up.
Keep an eye on http://hypothes.is. I think they plan to support private annotations, and handle PDFs through pdf.js. It doesn't have an offline document management component, but it could be used as the annotation component in a larger system.
I spent some time a few months back researching ways to have electronic PDFs which I could annotate and keep on my tablet. Mendeley was far and away the best. Here's hoping someone else figures this out.
https://forums.zotero.org/7/
Or build it yourself if so inclined/able:
http://www.zotero.org/support/dev/sample_plugin
http://www.zotero.org/support/dev/svn_and_trac_access