Right now if I install a JRE, I still can't run java applets in mozilla until I make a /usr/lib/mozilla-1.4/plugins/libjavaplugin_oji.so symlink. Ideally each JRE would supply this symlink via alternatives, so that java applets would work with no further configuration.
That should be /usr/lib/mozilla/plugins, _not_ /usr/lib/mozilla-<version>/plugins.
Verified, but note that there are no plugins available for non-x86 machines.