I have set a custom favicon on a Force.com site, but it is only working on the public site. The secure site still displays the default Salesforce favicon.
<mycompany>.force.com/favicon.ico
is the custom favicon, but <mycompany>.secure.force.com/favicon.ico
is the standard SF favicon.
From this question in the SF discussion forums, I understand that the custom favicon should take affect in a secure site if the site has no path. Yet, it is not working in our case.
For now, I'm adding <link rel="icon" href="{!$Resource.Favicon}" />
to the site template. However, I would prefer to do it declaratively if possible.