Re-Enable Apple Java 6 SE from Command Line?
Two things are needed worst case (and assuming you are still on 10.6 Snow Leopard):


Re-download the SE 6 and install it
Manually enable browser plug in if you care to have that functionality:



 ln -sf /System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPlugin2_NPAPI.plugin "/Library/Internet Plug-Ins/JavaAppletPlugin.plugin"
 ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws



There is great coverage of the how and why I came up with these steps from Rich Trouton's blog:


Re-enable the Apple Java 6 plug-in for use with web browsers
Java for OS X 2012-006 and Java for Mac OS X 10.6 Update 11


Apple also has similar steps in their KB article about the move from SE 6 to 7 here:


Java for OS X 2012-006: How to re-enable the Apple-provided Java SE 6 applet plug-in and Web Start functionality