After adding a theme to my desktop I noticed that the programs that run as root (Synaptic, log viewer, etc) all had the relatively ugly default GTK look (ugly_pic.png)
I created the .themes and .icons directories and copied the contents of the ones in my home directory into them.
sudo mkdir /root/.themes
sudo mkdir /root/.icons
sudo cp -r /home/${USER}/.themes/* /root/.themes sudo
cp -r /home/${USER}/.icons/* /root/.icons
I'm sure there may be more directories that need to be copied for other themes.