All I know is that some radio websites won't run unless I use Java. Click-to-Flash doesn't do it. I can't remember where I got the Java, if I downloaded it or it came with Adobe Flash when I downloaded that. But I needed Java to play the music.
Starting with Java 1.6.0_37, there is no Java Preferences app any more. It's in the release notes for the OS X Java update:
"This update also removes the Java Preferences application, which is no longer required to configure applet settings."
So if you have a version of the Java Preferences app on your computer, it's an older version, intended for an older version of Java. I have seen scattered reports that you can run it on modern OS X systems and change the settings, but it doesn't actually do anything.
