Curious how other people use Paperpile. I use it for five very different purposes: (1) to gather and organize my PDFs, (2) to organize my reading and research, (3) to format citations and bibliographies for publication, (4) to share documents with students and colleagues, and (5) to sync with my iPad for reading and annotating PDFs. As of now I have over 1000 items in Paperpile, of which only 50% (500) are Journal Articles with PDFs. The rest include many books, book chapters, thesis, conference papers, web pages, etc.
Regarding organizing my items, I have several tags that start with "#" which I use to assign status and priority to items, such as #urgent, #done, #toread, #someday, etc. I then have a number of topic related tags ("sociolinguistics," "Taiwan," "politics," etc.) and folders for individual projects or people (there are some scholars whose work I refer to a lot and need to access quickly).
Having just completed a 4 month research/writing project (first draft) with Paperpile, I feel that it meets my needs better than other reference managers I've used previously. The simply user interface, the tight integration with the browser, and the powerful citation formatting tool in Google Docs have been great for me.
My biggest unmet need is for a full fledged mobile interface that would let me add, share, and label items on my iPad. I know something is in the works, and look forward to that (although I know it will take some time). The other thing I look forward to is more robust search tools and filters. I really miss Sente's "smart folders" which (along with an iPad app) was one of my favorite features in Sente. Finally, I would really like to see the ability to generate plain-text citation markers that could be used in documents other than Google Docs, but which could then be scanned after being uploaded to Google. I like to work in plaintext (e.g. using ByWord or OS X and iOS) and it would be great if this could work better with Paperpile. But as it is, Paperpile is already my favorite citation manager. And I say that as one who has tried and used just about every product on the market. I'm glad to see increased activity on these forums and hope that Paperpile is able to succeed without getting bought out by a big company (my biggest fear).