I tend to keep my e-books and research papers in different piles in one sense. Calibre handles the e-books better than just about anything else out there. For

I tend to keep my e-books and research papers in different piles in one sense. Calibre handles the e-books better than just about anything else out there. For research papers I use DEVONThink. I tend to be a bit of a research paper pack-rat and DT makes it easy for me to find what I want in my huge slushpile of PDFs. The current DT iOS app is a bit of a work in progress, but until it gets to the same level us usefulness that the desktop version of DT had I can easily dump papers for mobile reading via the Dropbox->GoodReader path.