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JTourBus is an Eclipse plugin for navigating source code based on the idea of tours. Tours can be created using JavaDoc-tags (technically annotations work as well) supported by a little UI.
Jdeluxe is an Eclipse Plugin that helps developers to analyse B2B interfaces based on XML Standards. It is designed to be highly adaptable and uses generic XQuery-calls to extract documentation data. Data can be stored in a Web Repository via Web Service
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.