CommAPI for Linux
Free drivers for Sun's official serial driver interface: CommAPI, allowing you to use Linux serial (and eventually parallel ports) in an OS independent manner. [Open Source, LGPL]
Java Socket Interface for Infrared Communication
Allows Java programs on Linux to communicate via infrared ports, using infrared support in Linux kernels 2.2.14-irda1, or 2.3.48 or higher. [Open Source, LGPL]
JDX
A Java environment that allows Java programmers to build and extend a windowing system written mostly in Java and C. [Open Source, GPL]