Calibre is a free and open source e-book library management application developed by users of e-books for users of e-books. It has a cornucopia of features divided into the following main categories: Library Management - E-book conversion - Syncing to e-book reader devices - Downloading news from the web and converting it into e-book form - Comprehensive e-book viewer - Content server for online access to your book collection
Utopia Documents v2.2, is a free PDF reader that connects the static content of scientific articles to the dynamic world of online content.
See also pdfx v1.0 > http://pdfx.cs.man.ac.uk/ a fully-automated PDF-to-XML converter for scientific articles. It takes a full-text PDF article as input and outputs the hierarchy of its distinct logical elements in an XML format.