ClimbLog is a Java application for writing down climbing routes in something like a diary. The entries are stored hierarchically, so it's easy to navigate and search through the tree. You can add comments for each entry or tally routes. The data is stored in XML format and can be exported to HTML.
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.
JSX serializes Java objects to XML. You can persist objects, evolve them, and send them over the network and between applications. Your object data becomes human-readable and human-writable. You can test it, search it, profile it, audit it, and edit it with ordinary text and XML tools. JSX handles all POJOs and also all classes that require Java's own object serialization.
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.