Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Papermerge DMS - Open source document management system designed for archiving and retrieving your digital documents. Instead of having piles of paper documents all over your desk, office or drawers - you can quickly scan and upload them to Papermerge DMS.

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

Paperless-NG - A supercharged version of paperless: scan, index and archive all your physical documents - jonaswinkler/paperless-ng

Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.

Paperless - Developers and publishers of Mac, Win, and iOS productivity, home and office and writing software such as MacGourmet, Paperless, MacJournal and many more. Based in MN.