Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Simple Scan - Project information. Part of: The Gnome Project. Maintainer: Simple Scan Development Team. Driver: Simple Scan Development Team. Licence: GNU GPL v3.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
XSane - A good proposal for SANE-2 has been written.
EndNote - Accelerate Your Research. Save time, stay organized, collaborate with colleagues and get published with EndNote 20.
NAPS2 - NAPS2 is a document scanning application with a focus on simplicity and ease of use.