The Safari updates, version 6.0.4 for OS X Mountain Lion and Lion, and 5.1.9 for OS X Snow Leopard, bring a host of stability improvements to Apple's Web browsing software, including the ability to enable Java on a site-by-site basis.
As for the Java updates, Apple released assets for OS X Mountain Lion and Lion, as well as an updated for OS X Snow Leopard.
From the Java for Snow Leopard release notes:
Java for Mac OS X 10.6 Update 15 delivers improved security, reliability, and compatibility by updating Java SE 6 to 1.6.0_45. This update enables website-by-website control of the Java plug-in within Safari 5.1.9 or later.
The Java for OS X updates for Mountain Lion, Lion and Snow Leopard bring support for the latest Java 6 update 45 from Oracle.
Java for OS X 2013-003 and the OS X 10.6-specific updates can be downloaded via Software Update or Apple's Support webpage.