PdfHighlights - PdfHighlights extracts and exports all your PDF highlights and PDF annotations from all your PDF files into a single report.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
PDFelement Pro - PDFelement Pro is a feature-rich and highly useful solution that enables you to modify, populate, convert, sign and annotate PDFs.
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.
LiquidText - LiquidText improves upon the reading experience by allowing users to better synthesize, visualize and collaborate over digital text.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .