Since x3 there are no more evil HTML files to update.  Instead, you can create plugins to add your own icons to cPanel to link off to other sites or features.  cPanel now has a nice little plugin generator where you can  upload the image and specify where the link will go:

http://www.cpanel.net/plugins/devel/install.htm

Once you’ve created one, you would register the plugin according to cPanel’s instructions and activate it in your feature manager.