With this latest update, Apple has made some significant changes to the Java runtime. Oracle's Java System Preferences contains similar options for enabling, disabling, and otherwise configuring the installed Java runtimes. In fact, leaving out Java Preferences is a part of Apple's progressive move away from in-house support for Java. 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. 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. 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. 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.
