 <p>It seems to be the file <code>C:\Users\%USER%\AppData\LocalLow\Sun\Java\Deployment\deployment.properties</code> where the command line arguments are stored.</p> <p>Adding <code>test123</code> in the command line arguments changes the file to the following:</p> <pre><code>deployment.javaws.jre.1.location=http\://java.sun.com/products/autodl/j2se deployment.javaws.jre.1.args=test123 deployment.javaws.jre.1.enabled=true deployment.javaws.jre.1.registered=true deployment.javaws.jre.1.product=1.6.0_22 deployment.javaws.jre.1.path=C\:\\Program Files\\Java\\jre6\\bin\\javaw.exe deployment.javaws.jre.1.osarch=amd64 deployment.javaws.jre.1.osname=Windows deployment.javaws.jre.1.platform=1.6 </code></pre> <p>At least, I can manually edit the file and the changes show up in the Java Control Panel. The file's documentation can be found <a href="http://download.oracle.com/javase/6/docs/technotes/guides/deployment/deployment-guide/properties.html">here</a>.</p>