NAPS2 - NAPS2 is a document scanning application with a focus on simplicity and ease of use.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
TeraCopy - TeraCopy is a compact program designed to copy and move files at the maximum possible speed, providing the user with a lot of features.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Genius Scan - On The Go.
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.