Safari 6.0.4 allows users to enable the Java plug-in for Safari on a website-by-website basis.
For detailed information about this update, please visit: http://support.apple.com/kb/HT5678
Java for OS X 2013-003 1.0:
Java for OS X 2013-003 delivers improved security, reliability, and compatibility by updating Java SE 6 to 1.6.0_45. On systems that have no already installed Java for OS X 2012-006, this update disables the Java SE 6 applet plug-in. To use applets on a webpage, click on the region label "Missing plug-in" to download the altest version of the Java applet plug-in from Oracle. Please quit any web brwosers and JAva applications before installing this update.
See http://support.apple.com/kb/HT5682 for more details about this update.