Mountain Lion 10.8.2, Java Preferences has disappeared I just installed the latest Java update from apple (Java for OS X 2012-006) and I was looking to have a look at what's going on with my java(s) with Java Preferences app (which used to live in /Applications/Utilities though it seems it has now disappeared.  Any idea on whether there is a problem with my system or did the update clobber Java Preferences?
The update in question (Java for OS X 2012-006) disables the Safari Java plugin for security purposes. Per Apple technical bulletin:


  This release updates the Apple-provided system Java SE 6 to version
  1.6.0_37 and is for OS X versions 10.7 or later.
  
  This update uninstalls the Apple-provided Java applet plug-in from all
  web browsers. To use applets on a web page, click on the region
  labeled "Missing plug-in" to go download the latest version of the
  Java applet plug-in from Oracle.
  
  This update also removes the Java Preferences application, which is no
  longer required to configure applet settings.


Here is an Apple technical bulletin link on how to re-enable the plugin

If you need the full Java runtime you may download it directly from Oracle by going this webpage.