Having recently switched from Firefox 2 to Firefox 3, I found that the Java Plug-In was no longer working. Looking at the list of browser plugins being used by Firefox 3 (enter "about:plugins" in the browser's navigation field) I discovered that the OpenJDK GCJ was being used rather than Sun's JRE v6.0 plugin (from the sun-java6-* packages).
It took some time to work out why this was the case - /usr/lib/firefox/plugins contained a symbolic link to /etc/alternatives/mozilla-firefox-javaplugin.so, which in turn was set to Sun's JRE v6.0 plug-in.
The only Java Plug-In alternative set to OpenJDK's was that of xulrunner-1.9. So, I changed it's setting to Sun's JRE v.6.0 of the plugin:
sudo update-alternatives --config xulrunner-1.9-javaplugin.so
and upon restarting Firefox 3 it used Sun's Java Plug-In.
Very weird, and possibly related to this bug?