We make use of a java application that manages a pinpad via the serial port. This works perfectly on windows with the Sun Comm.jar, the supplied dll and the properties file.
We've been using the SerialIO libraries for Java serial communications on both Windows and Linux for several years now with great results (and no, I don't work for them :-)):
http://serialio.com/products/serialport/serialport.php
The libraries do not autodetect the available serial ports on Linux though - you have to manually configure them.