java -cp jutils.jar:jinput.jar:somePlugin.jar -Djava.library.path=. -Djinput.plugins=the.name.of.the.PluginClass the.class.to.Run
This assumes that the native library (e.g. dxinput.dll) is in the directory from where you are calling this.
Jeff's plugin mechanism may be nice but IMHO causes to much hassle especially if you have multiple JVMs installed.
The names of the plugin classes are listed on the introduction page.