Apple released updates to Safari today that allow users to enable the Java plug-in on a per website basis. We generally recommend that users keep Java disabled, but in the event that you do need it, you can now choose when you want to use it.
When using Safari 6.0.4 (Mac OS X 10.7 and 10.8) and Safari 5.1.9 (Mac OS X 10.6), if you should go to a site that attempts to load a Java applet, a dialog box will appear on your screen to ask if you want to block or allow the Java applet. You can also view a list of websites that have attempted to load Java applets by going to Preferences in Safari, clicking on the “Security” tab, and then clicking “Manage Website Settings…” You can then choose to block or allow these sites to use Java plug-ins.
There’s also a Java for OS X 2013-003 update that provides improved security by updating Java SE 6 to 1.6.0_45. Per Apple’s notes:
“On systems that have not already installed Java for OS X 2012-006, this update disables the Java SE 6 applet plug-in. To use applets on a web page, click on the region labeled “Missing plug-in” to download the latest version of the Java applet plug-in from Oracle.”