I needed to install a Java plugin for Firefox under Ubuntu 9.04 (beta). This didn’t happen by itself when I installed sun-java6-plugin, but a quick search showed me what Eirik Hoem found out a year ago.
Or, as Karl Trygve said in a comment; messing about in /usr is usually not a good idea
– the link could be made in /usr/lib/firefox-3.0/plugins, and the plugin would then be available for all users on the computer.
Linking the java plugin to Firefox (paths might vary a bit, depending on Java versions):
cd ~/.mozilla/firefox/.default/plugins
sudo ln -s /usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so
I didn’t have Icedtea installed, but I do use OpenJDK for development. Works now, at least. 
Messing about in /usr is usually not a good idea, but the advantage is that now all users on the machine will get the Java plugin enabled in their Firefox.
If you only wanted to enable it for your own user, the symlink can be placed in .mozilla/firefox/.default/plugins
Thanks. I guess it is something I did that stopped it from registering normally, but still.
I’ll update the post with the profile path.