Emerald:
Emerald wasn't actually changing my windows even though a different theme was highlighted. So add the following (as a new startup program) to sessions (Systems-->Preferences-->Sessions):
emerald --replace
Java:
I was using sun's version of java but it wasn't working for me on firefox and I found this thread to help. First if you want to use sun's version, install the following packages: sun-java6-jre and sun-java6-plugin. To get it to work, first try uninstalling the package icedtea-gcjwebplugin. Then restart firefox and test again on the java webpage. If that doesn't work, try also uninstalling openjdk-6-jre. That did it for me.
System-Config-Samba:
For anyone that doesn't know, this package makes Samba configuration incredibly simple. (As a side point, I will show possible settings in a separate future post). However, the samba config utility wasn't working. Here's what I had to do. Run the following command:
sudo touch /etc/libuser.conf
Thanks to Ubuntu Forums for the answers.