To change favicon you need edit lib/perl5/site_perl/5.8.8/IkiWiki/Plugin/favicon.pm and change line:
> $template->param(favicon => "favicon.ico");
 
at the end of file. And rebuild wiki:
> ikiwiki -setup your_wiki_config

After reload page you'll see your new favicon.

That method allow configure Animated PNG even:
> ikiwiki.sphynkx.org.ua

----
Sphynkx

> Typically sites that use animated pngs (ugh!) as favicons just call it
> `favicon.ico`. It's not as if (most) web servers and browsers trust
> the filename extension to mean anything anyway. And using favicon.ico
> makes it more likely to work with old browsers that just always look for
> that. --[[Joey]]