Worthy of further study:

Webwork is an MVC framework along the lines of struts, but smaller and cleaner, with less servlet-specificness.

Xindice is a native XML database that allows the use of XPath for queries.

Kodo is a JDO implementation that makes persistence look really easy.

Sitemesh is a dynamic decoration framework for HTML pages.

Lucene is a java based document indexing system and full text search engine.