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TeX4Java is a parser for the TeX language written in Java. The boxworld is created as Java objects providing an API to create own representations of the document. TeX4Java includes two representations as well: TeXImage and TeXPresenter.
JBib2HTML is a Java based software that converts bibtex files to HTML format. It comes with predefined conversion templates and is easily extensible so that you can create your own custom implementations of exports.
Paper2bibtex is a modular information harvester implemented in Java which extracts name and author information from scientific papers (PS or PDF), adds paper meta information from public internet sites and compiles a bibliography entry for bibtex
Eclipse PDF Renderer is a plugin for the Eclipse IDE. It adds a view to Eclipse in which PDF documents can be displayed. It might be useful if your Eclipse workspace contains several PDF files, or if you're using other Eclipse plugins like texlipse.
BibTeXlipse is an Eclipse plugin for managing and analyse bibliography databases. Mainly for BibTeX databases, but will import and export many other bibliographic formats.
It's currently in planning phase.