A few corrections/additions to the message above.
1) The symbolic link in the folder "/etc/alternatives" is named 
"mozilla-javaplugin.so".
2) The folder "/usr/lib/jvm/java-6-sun" is a symbolic link to the actual 
java-sun folder like "/usr/lib/jvm/java-6-sun-1.6.0.16/"
     So actually the shared object "libnpjp2.so" is located in the folder 
"/usr/lib/jvm/java-6-sun-1.6.0.16/jre/lib/amd64".
3) There is also a symbolic link "libjavaplugin.so" in the folder 
"/usr/lib/xulrunner-addons/plugins" pointing to another symbolic link
     "xulrunner-javaplugin.so".

As a workaround to this bug (if the package sun-java6-plugin is installed) one 
should create two symbolic links:
1) /etc/alternatives/mozilla-javaplugin.so pointing to 
/usr/lib/jvm/java-6-sun/jre/lib/amd64/libnpjp2.so and
2) /usr/lib/mozilla/plugins/libjavaplugin.so pointing to 
/etc/alternatives/mozilla-javaplugin.so.

I have tested this with Lucid Lynx 64-bit with the browser firefox 3.6.1pre 
from the Mozilla daily build team PPA.
This makes java plugin actually be recognized and work OK.

-- 
java are not reconize by firefox 3.6 
https://bugs.launchpad.net/bugs/511151
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