ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
VRaptor 2 is a Web-based MVC and IOC framework based on many frameworks and ideas (Seam, Stripes, Webwork, Hibernate Annotations, etc). It makes full use of Java 5 Annotations. It favors convention over configuration, because configuration in XML/properties/annotations is always easy to make mistakes and repetitive (aka copy and paste in many places). This framework uses a more imperative approach, instead of having many XML files to configure lifecycle and other properties. Most of the settings go inside plain Java objects (POJO), so the team knows exactly what is going on and where.
JCons provides a library that bring color to your Java console. The Java console gives no methods to change the foreground or background color. With help of this library, one can make error messages red and success messages green, for example. Most Unix terminals can deal with ESC sequences, so they are used to make the Java console colorful.
Echomine Feridian is an easy-to-use Java API that gives you quick and easy access to the XMPP network used in IM services such as Google Talk. The API allows you to communicate with Jabber/XMPP servers for sending and receiving instant messages, presence management, and custom extensions to the XMPP protocol.
Wiseman is an implementation of the WS-Management specification for the Java SE platform. The project scope includes the WS-Management specification and its dependent specifications, which can be found at http://www.dmtf.org/standards/wbem/wsman/. The project requires Java SE 5+ or above, and is built on JAXB 2.0 and SAAJ 1.3 (part of the JAX-WS project). Ant scripts for standalone and Netbeans builds are supplied.
Apache XML Graphics Commons is a library that consists of several reusable components used by Apache Batik and Apache FOP. Many of these components can easily be used separately outside the domains of SVG and XSL-FO. You will find components such as a PDF library, an RTF library, Graphics2D implementations that let you generate PDF and PostScript files, and much more.