http://support.apple.com/kb/HT5678
The details are saved in ~/Library/Preferences/com.apple.Safari.plist as follows; this is an example of a saved site where Java is always permitted to run:
<key>WhitelistedBlockedPlugins</key>
<array>
<dict>
<key>PluginHostname</key>
<string>foo.company.com</string>
<key>PluginIdentifier</key>
<string>com.oracle.java.JavaAppletPlugin</string>
<key>PluginLastVisitedDate</key>
<date>2013-04-16T21:14:29Z</date>
<key>PluginName</key>
<string>Java Applet Plug-in</string>
<key>PluginPageURL</key>
<string>https://foo.company.com/somejavathing</string>
<key>PluginPolicy</key>
<string>PluginPolicyNeverBlock</string>
</dict>
</array>