The admin pages in v1.3.x don't share enough common code to allow you to generically make one single change that affects favicons or any other <head> section tags on all pages universally.

If you are happy to set it only for your admin home page, you can make the following alteration to your /admin/index.php file:
Code:
<head>
<meta http-equiv="Content-Type" content="text/html; charset=<?php echo CHARSET; ?>">
<title><?php echo TITLE; ?></title>
<meta name="robot" content="noindex, nofollow" />
<link rel="icon" href="/path/to/custom/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="/path/to/custom/favicon.ico" type="image/x-icon" />
<script language="JavaScript" src="includes/menu.js" type="text/JavaScript"></script>
You might consider similarly for the /admin/login.php file.

ALERT TO OTHERS WHO MIGHT READ THIS POST ... This code suggestion is ONLY for the ADMIN section. If you're mucking with favicons for your storefront, see the FAQ tutorial article for proper instructions there, since there is NO NEED to add these <link> tags in the storefront for favicon support.