I am using firefox-3.0 in Hardy, and when I check the plugins (from Tools->Addons or about:plugins) I found that the java plugin is GCJ. Although I have done 'update-java-alternatives -s java-6-sun', so when I check the output of this command I find the following:
No alternatives for firefox-plugins-javaplugin.so.
Using '/usr/lib/jvm/java-6-sun/bin/appletviewer' to provide 'appletviewer'.
Using '/usr/lib/jvm/java-6-sun/bin/apt' to provide 'apt'.
Using '/usr/lib/jvm/java-6-sun/bin/extcheck' to provide 'extcheck'.
Using '/usr/lib/jvm/java-6-sun/bin/HtmlConverter' to provide 'HtmlConverter'.
Using '/usr/lib/jvm/java-6-sun/bin/idlj' to provide 'idlj'.
Using '/usr/lib/jvm/java-6-sun/bin/jarsigner' to provide 'jarsigner'.
Using '/usr/lib/jvm/java-6-sun/bin/jar' to provide 'jar'.
Using '/usr/lib/jvm/java-6-sun/bin/javac' to provide 'javac'.
Using '/usr/lib/jvm/java-6-sun/bin/javadoc' to provide 'javadoc'.
Using '/usr/lib/jvm/java-6-sun/bin/javah' to provide 'javah'.
Using '/usr/lib/jvm/java-6-sun/bin/javap' to provide 'javap'.
Using '/usr/lib/jvm/java-6-sun/bin/java-rmi.cgi' to provide 'java-rmi.cgi'.
Using '/usr/lib/jvm/java-6-sun/bin/jconsole' to provide 'jconsole'.
Using '/usr/lib/jvm/java-6-sun/bin/jdb' to provide 'jdb'.
Using '/usr/lib/jvm/java-6-sun/bin/jhat' to provide 'jhat'.
Using '/usr/lib/jvm/java-6-sun/bin/jinfo' to provide 'jinfo'.
Using '/usr/lib/jvm/java-6-sun/bin/jmap' to provide 'jmap'.
Using '/usr/lib/jvm/java-6-sun/bin/jps' to provide 'jps'.
Using '/usr/lib/jvm/java-6-sun/bin/jrunscript' to provide 'jrunscript'.
Using '/usr/lib/jvm/java-6-sun/bin/jsadebugd' to provide 'jsadebugd'.
Using '/usr/lib/jvm/java-6-sun/bin/jstack' to provide 'jstack'.
Using '/usr/lib/jvm/java-6-sun/bin/jstatd' to provide 'jstatd'.
Using '/usr/lib/jvm/java-6-sun/bin/jstat' to provide 'jstat'.
Using '/usr/lib/jvm/java-6-sun/bin/native2ascii' to provide 'native2ascii'.
Using '/usr/lib/jvm/java-6-sun/bin/rmic' to provide 'rmic'.
Using '/usr/lib/jvm/java-6-sun/bin/schemagen' to provide 'schemagen'.
Using '/usr/lib/jvm/java-6-sun/bin/serialver' to provide 'serialver'.
Using '/usr/lib/jvm/java-6-sun/bin/wsgen' to provide 'wsgen'.
Using '/usr/lib/jvm/java-6-sun/bin/wsimport' to provide 'wsimport'.
Using '/usr/lib/jvm/java-6-sun/bin/xjc' to provide 'xjc'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/ControlPanel' to provide 'ControlPanel'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/java' to provide 'java'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/java_vm' to provide 'java_vm'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/javaws' to provide 'javaws'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/jcontrol' to provide 'jcontrol'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/keytool' to provide 'keytool'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/orbd' to provide 'orbd'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/pack200' to provide 'pack200'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/policytool' to provide 'policytool'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/rmid' to provide 'rmid'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/rmiregistry' to provide 'rmiregistry'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/servertool' to provide 'servertool'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/tnameserv' to provide 'tnameserv'.
Using '/usr/lib/jvm/java-6-sun/jre/bin/unpack200' to provide 'unpack200'.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'firefox-javaplugin.so'.
No alternatives for firefox-plugins-javaplugin.so.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'iceape-javaplugin.so'.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'iceweasel-javaplugin.so'.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'midbrowser-javaplugin.so'.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'mozilla-javaplugin.so'.
Using '/usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so' to provide 'xulrunner-javaplugin.so'.
So it seems that update-java-alternatives does not handle alternatives for firefox-addons-javaplugin.so
Make sure you've also added the plugin:
sudo aptitude install sun-java6-plugin