<p>By default, Eclipse won't show my .htaccess file that I maintain in my project.  It just shows an empty folder in the Package Viewer tree.  How can I get it to show up?  No obvious preferences.</p>

In your package explorer, pull down the menu and select "Filters ...".  You can adjust what types of files are shown/hidden there.
Looking at my Red Hat Developer Studio (approximately Eclipse 3.2), I see that the top item in the list is ".* resources" and it is excluded by default.