A `sunrise.php` drop in that (mostly) allows custom domains in WordPress multisite. Still needs some more work, but it gets the job done.

sunrise.php

<?php
/**
 * A sunrise.php drop in that allows you to use WordPress' built in `domain`
 * and `path` settings for MultiSite blogs.
 *
 * Some limitations:
 *  - Using this with a MS install and paths (not subdomains) does some
 *    weird stuff when updating `siteurl` and `home` while updating domain.
 *    So you'll you'll have to update those separately. There are probably
 *    filters to fix this.
 *  - Each blog's `siteurl` should still include the path to WordPress if you
 *    have WP installed in a subdirectory. The site will still work without
 *    this, but going to wp-admin on that site will not.
 *  - You can only have a single domain (and it's matching (non-)www partner)
 *    per site.  This probably isn't a big deal: it's supid to build the
 *    same site on more than one domain.
 *  - Non-apache folks may have a more difficult time with permalinks. I couldn't
 *    get rid of `index.php` using nginx -- WordPress kept adding it back in.
 *
 * @author      Christopher Davis <chris [AT] classicalguitar.org>
 * @license     GPLv2
 */

if(defined('COOKIE_DOMAIN') || defined('SITECOOKIEPATH'))
{
    die('"COOKIE_DOMAIN" or "SITECOOKIEPATH" is defined.');
}

$dm_domain = $_SERVER['HTTP_HOST'];

if(($nowww = preg_replace('/^www\./', '', $dm_domain)) != $dm_domain)
{
    $where = $wpdb->prepare('domain IN (%s, %s)', $dm_domain, $nowww);
}
else
{
    $where = $wpdb->prepare('domain = %s', $dm_domain);
}

if($_blog = $wpdb->get_row("SELECT * FROM {$wpdb->blogs} WHERE {$where} LIMIT 1"))
{
    $current_blog = $_blog;

    $blog_id = $_blog->blog_id;
    $site_id = $current_blog->site_id;

    $current_site = $wpdb->get_row(
        $wpdb->prepare("SELECT * from {$wpdb->site} WHERE id = %d", $site_id)
    );
    $current_site->blog_id = $blog_id;

    $current_site = get_current_site_name($current_site);

    define('COOKIE_DOMAIN', $_SERVER['HTTP_HOST']);
    // WP uses $current_site->path to define this. We don't want that.
    define('SITECOOKIEPATH', $current_blog->path);
}

There's no reliable way to get the HTTP_HOST, but here's a maybe more safe way:

! empty( $_SERVER['SERVER_NAME'] ) AND $domain = $_SERVER['SERVER_NAME'];
! isset( $domain ) AND ! empty( $_SERVER['HTTP_HOST'] ) AND $domain = $_SERVER['HTTP_HOST'];

#fail and abort
if ( ! isset( $domain ) )
    return;