Java Web Start allows certain JVM flags to be set with the java-vm-args attribute of the j2se element but you may use

<property name="key" value="overwritten"/>  

and set properties. it will be available through the System.getProperty and System.setProperties methods

http://java.sun.com/j2se/1.5.0/docs/guide/javaws/developersguide/syntax.html#resources