In Java we use System.setProperty() method to set some system properties. According to this article the use of system properties is bit tricky.
System
You don't say what your motivation is for using system properties.
We use Spring for our configuration and set initial properties using a properties file that is injected into the XML. Changes to configuration whilst the app is running are made by using JMX.
There are - of course - many other ways to change configuration in Java using properties file, xml based configuration etc.