For Genesis Child Themes in Multisite -- one child theme for lots of sub sites: Pull in site-specific functions & stylesheet files, if available.

multisite-functions.php

<?php

/**
 * General Usage:
 *  Set "child-theme-slug" to the main child theme slug. Set "id" to actual Blog/ Site ID.
 *  Current: For Multisite installs that were made with 3.5+
 *  a) Place functions files in wp-content/uploads/sites/{id}/{child-theme-slug}/functions-site-{id}.php
 *  b) Place stylesheet files in wp-content/uploads/sites/{id}/{child-theme-slug}/styles-site-{id}.php
 *
 *  Backward compatibility for Multisite installs that were made prior 3.5
 *  c) Place functions files in wp-content/blogs.dir/{id}/files/{child-theme-slug}/functions-site-{id}.php
 *  d) Place stylesheet files in wp-content/blogs.dir/{id}/files/{child-theme-slug}/styles-site-{id}.php
 *
 * @author David Decker - DECKERWEB
 * @link   http://deckerweb.de/twitter
 */


/**
 * Get the Blog/ Site upload location location for URL or path, and for multisite or not.
 *
 * Takes account of multisite usage, and domain mapping.
 *
 * @author StudioPress
 * @link   http://www.studiopress.com/
 * @author David Decker - DECKERWEB
 * @link   http://deckerweb.de/twitter
 *
 * @param string $type Either 'url' or anything else e.g. 'path'
 *
 * @return string
 */
function ddw_get_site_upload_location( $type ) {

	/** Get the uploads directory -- supports Multisite of course */
	$uploads = wp_upload_dir();
	$dir = ( 'url' == $type ) ? $uploads['baseurl'] : $uploads['basedir'];

	$child_slug = wp_get_theme();

	/** Return Blog/ Site upload location */
	return apply_filters( 'ddw_get_site_upload_location', $dir . '/' . $child_slug . '/' );

}  // end function


add_action( 'after_setup_theme', 'ddw_include_site_specific_functions', 10 );
/**
 * Pull in site-specific functions files, if available.
 *
 * @author David Decker - DECKERWEB
 * @link   http://deckerweb.de/twitter
 *
 * @param  $site_file
 *
 * @global integer $blog_id 
 */
function ddw_include_site_specific_functions() {

	/** Get the Blog/ Site ID within Multisite */
	global $blog_id;

	/** Set a site specific functions file */
	$site_file = ddw_get_site_upload_location( 'path' ) . 'functions-site-' . $blog_id . '.php';

	/** Check for file and include it */
	if ( is_readable( $site_file ) ) {

        	require_once( $site_file );

	}  // end if file check
	
}  // end function


add_action( 'wp_enqueue_scripts', 'ddw_include_site_specific_scripts', 10 );
/**
 * Pull in site-specific scripts or stylesheet files, if available.
 *
 * @author David Decker - DECKERWEB
 * @link   http://deckerweb.de/twitter
 *
 * @param  $site_file_path
 * @param  $site_file_url
 *
 * @global integer $blog_id 
 */
function ddw_include_site_specific_scripts() {

	/** Get the Blog/ Site ID within Multisite */
	global $blog_id;

	/** Set a site specific functions file */
	$site_file_path = ddw_get_site_upload_location( 'path' ) . 'styles-site-' . $blog_id . '.css';
	$site_file_url = ddw_get_site_upload_location( 'url' ) . 'styles-site-' . $blog_id . '.css';

	/** Check for file and include it */
	if ( is_readable( $site_file_path ) ) {

		/** Register the stylesheet */
		wp_register_style( 'site-styles', $site_file_url, array(), time(), 'all' );

		/** Enqueue the stylesheet */
wp_enqueue_style( 'site-styles' );

	}  // end if file check
	
}  // end function