For the longest time I used .htaccess to shunt my favicons to the right place based on the requesting domain. This basic logic worked well, but was starting to get weird and it didn’t always work depending on if I was using pagespeed to trim out leading domains or not, and of course when I tightened security it got weirder.
Now I’ve know you can use custom favicon in Genesis and that’s pretty simple. But … I have to make my life complicated. See I use Multisite and I don’t edit my themes. No, really, this theme? I only edited it to update it. I don’t edit them, I use custom CSS and functions to edit via hooks and filters, the way you’re supposed to.
So how do I override favicons for five sites on a Multisite? Why with an MU Plugin!
wp_head() and toss in the link for shortcut icon.