How to manage my pdf files?

Looking for the best software and tools for academics working with digital files

• I'm giving a workshop to a group of humanities scholars (historians, philosophers, etc) on how to work with digitized sources that they have collected from various archives. What killer software/apps should I highlight? I'm a librarian in a specialized research archive, and I work with historians and other scholars who often compile enormous personal collections of digitized files (primary and secondary sources, usually JPGs or PDFs) in the course of their research. I will be giving a brief (1.5 hour or so) workshop on how to wrangle these files into a system that works for them and allows them to spend their time analyzing and writing instead of, say, looking for an old file they remember seeing a few months ago. I'll be covering things like backup options (Google Drive, Dropbox, etc), file formats (e.g. print to PDF options for JPGs), and naming conventions, and will be spending a lot of time on reference and file management software (like http://www.mekentosj.com/papers/, http://www.mendeley.com/, http://www.zotero.org/, http://www.qiqqa.com/, and http://www.thirdstreetsoftware.com/site/SenteForMac.html). My goal is to cover to the stages of working with digital files (capturing, manipulating, backup, and analyzing), introduce various approaches and software options for each step, then encourage them to develop a system that works for them and their specific needs. What killer software or apps might I have overlooked that might help them? I'm mainly just introducing various programs and approaches, so even a brief reference like "some people really like [Program X]" is enough. Free or relatively cheap would be preferred, but if the best program for their purposes isn't free I still want to mention it. A couple notes: I will not be discussing OCR much, because most of the documents these people are working with are in other languages (German, Polish, Hebrew and Russian, mainly) and the source files are often handwritten or poorly-microfilmed. Also, remember that I'm talking to scholars about their individual projects, not librarians or archivists looking to manage large digital collections, so "best practices" for institutions are not as relevant here. I've learned a lot in the course of assisting my girlfriend with her research (as discussed in this http://ask.metafilter.com/200904/Help-me-find-the-best-PDF-management-software-for-a-PdD-researcher about reference management software), but I'm sure that there are new tools I haven't used. Any pointers would be greatly appreciated!

• Answer:

  For those who are already reading books on their kindles, http://clippingsconverter.com/kindle-clippings-blog is a priceless thing. It takes your clippings and notes made on the kindle and converts them to an excel, word, pdf or evernote file. For me, the excel spreadsheet was the most awesome way to keep track of all my notes for my dissertation. I loved it and that combined with Zotero was the most flawless and painless way to do research I can imagine.