JDB is package of commands for manipulating flat ASCII databases from shell scripts. It is useful to process medium amounts of data (with very little data, you'd do it by hand; with megabytes, you might want a real database). It is very good at doing things like managing data for research experiments. By storing data in simple text files and processing it with pipelines, it is easy to experiment (in the shell) and look at the output.
JReferences is a program written in Java for managing bibliographic references in the BibTeXML format. Storage is done in a binary file database or, optionally, in a MySQL database. A PHP Web frontend is available. It can input BibTex, RIS, BibTeXML, and DocBook formated references.
Java Serialization to XML (JSX) serializes/deserializes Java objects to/from XML, so you can save them, send them - and see them! It correctly handles the many Serializable classes in Java and third-party libraries that use Java's builtin Java Object Serialization (JOS) to customize their serialization (for security, validation, faithful deserialisation, and class evolution).
JTOpen is the open source version of the IBM Toolbox for Java. This set of Java classes allows any Java-enabled client to access data and resources on an iSeries or AS/400 server. It contains a JDBC driver, FTP, remote command invocation, SSL support, and tons of other functionality. It also includes GUI wrappers for most functions, a runtime PCML interpreter, and an XML parser. Most of the classes are available as open source, and the binaries are free to download and distribute.