Apple has recently released a couple of Java updates for OS X 10.6, 10.7, and 10.8 that bring its in-house supported Java runtime (Java SE 6) up to the latest version issued by Oracle. The update tackles a couple of security bugs in the runtime, but those who have installed the updates have noticed that in addition Apple has apparently removed the Java Preferences utility, which was used to configure how the Java runtime is managed in OS X.
While Java Preferences is missing for those using OS X 10.7 or later, the utility is still present for those who update Java in OS X 10.6. This may seem to suggest that Apple simply overlooked including Java Preferences in the updater for OS X 10.7 and later; however, this is not the case. In fact, leaving out Java Preferences is a part of Apple's progressive move away from in-house support for Java.
With this latest update, Apple has made some significant changes to the Java runtime. One of the first is that while the Java 2012-006 updater will install the latest version of Java SE 6, it will configure the Web plug-in to download the latest Java 7 runtime from Oracle when applets are run. This step will hopefully migrate more users to the latest developments from Oracle instead of relying on Apple for Java support.
In addition, the various Java tools Apple includes (such as command-line tools) are configured with reference to the Java runtime with the highest version number, ensuring that Java 7 or later will be used once it is installed, regardless of any other runtimes that may be present. Since Java from Oracle has its own configuration tools and does not use Apple's Java Preferences utility, Apple has removed this utility in favor of Oracle's tools.
Unfortunately Oracle will only be supporting OS X 10.7 and later with Java 7, so Apple has left these changes to the runtime out of Java for Snow Leopard. Therefore, these users will have Apple's Java Preferences utility available for this and future updates to Java SE 6.
While Apple's Java Preferences utility can be restored from a Time Machine backup and used to configure any installed runtimes, this shouldn't be necessary. In short, if you have OS X 10.7 or later and wish to configure Java after applying this update, then you'll be using Oracle's Java system preferences pane.