A simple way to prevent running of multiple instances of your application is to use Socket communication. For example, in Groovy the first thing you would execute is something like this:

try {
    // choose a unique port (!!)
    new Socket('localhost', 1337)
    println 'Already running'
    System.exit(0)
}
catch (Exception e) {
}

Following this, another block of code initialises the server socket to indicate an instance is running:

Thread.start {
    ServerSocket server = [1337]
    while(true) {
        try {
            server.accept {}
        }
        // extra actions such as bring window to front
        // on the running app may be performed here..
        finally {
            ousia.doLater {
                frame.visible = true
            }
        }
    }
}

Of course the same can be done in Java, just not in such a concise way.