If you install the latest Java update, released yesterday, on OS X Lion or OS X Mountain Lion, it will not only delete the Java web-plugin, but it will delete something you didn’t expect… Java Preferences.app.
Apple did make note of this, in the security descriptor notes for the update, but nowhere in the notes that an ordinary user would read. Java Preferences.app is the tool that enables you to select which JDK you are using to run apps on the desktop. Apple claims the app is “no longer needed” (their words). I disagree.
Obviously, if you need to toggle between Java 6 and Java 7 for testing apps, this tool might be of some use to you. In Apple’s defense, you can still do this from the Terminal, but it takes a lot longer and is just a very un-Apple experience.
Of course, Apple doesn’t want much to do with Java anymore, so making the experience un-Apple is all part of the plan.
Anyways, to preserve Java Preferences.app, go into /Applications/Utilities and copy the Java Preferences.app file somewhere else, even just /Applications. Then run the latest Java update. Finally, go to Java.com and grab the latest JRE (which remember, on Mac is just a web browser plugin) and JDK (which remember, is needed to run desktop apps on Mac).
Java on Mac users, while you can.