As an academic writer, I rely in large parts on supportive evidence as integral parts of my writing process. This evidence comes in various shapes and forms: PDFs of journal articles, notes I have taken from other sources, data in table form or graphs, etc. Often, this involves collaborative work and work in progress (especially data). One of the best solutions to integrate such “assets” or “evidence” I have found is Google Docs that allows me to work in collaboration with others or on my own (but from various places, my office, the library, etc.).
In addition to the normal set-up in Scrivener, I add specific documents and spreadsheets to a “Data” folder I have set up in the Research section of Scrivener. As of yet, Google Docs does not work in Safari (which will change soon, I am sure), but you can view and edit individual documents as well as spreadsheets (although the spreadsheets don’t really work that well). Once you are ready to use a part of such an asset in your Scrivener document, you simply copy and paste. Alternatively, you can export your document in Google Docs and import it into Scrivener (if you prefer that).
The integration could be somewhat improved, of course (for example, I still haven’t figured out who to change the viewing options in Scrivener of an imported web page), and the ultimate integration would be a “live” PDF-kit based browser in Scrivener for such an integration to work. But as of now, this solution works pretty well for me, given that I can add notes from everywhere I have access to the web (e.g., the library), but not necessarily to my Scrivener document or when I collaborate with others.