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PDFTK Builder - PDFTK Builder is a free graphical interface to for PDFTK, making it much easier to use.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
PDF Arranger - Small python-gtk application, which helps the user to merge or split pdf documents and rotate, crop...
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
PDF Joiner - This online tool allows you to join several PDF documents into a single file, free of charge.
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.