Drush auto-alias script. This script, when placed in your /etc/drush folder will scan your webroot and auto-detect Drupal installations, both standalone and multisite, and create aliases for each site. It is not complete yet. The grouping still needs a little work, but otherwise gets you off the ground.

aliases.drushrc.php

<?php
/**
 * @file
 * Build a dynamic list of drush aliases by identifying Drupal directories.
 *
 * The script will scan your webroot for Drupal directories.  Place this in
 * /etc/drush/aliases.drushrc.php
 *
 * @param $root
 *   The absolute path to your webroot.
 */
// Webroot
$web = "/var/www/htdocs";

// Instantiate the alias arrays.
$aliases = $auto_aliases = array();

// The current directory will be either the actual directory if not in a drupal
// root or the drupal root directory if we are anywhere within a drupal site.
$cwd = getcwd();

/**
 * Helper function to parse out site overrides.
 */
if (!function_exists('_daconfig_get_settings')) {
  function _daconfig_get_settings($path) {
    if (file_exists($path)) {
      include($path);
    }

    $custom = array(
      'aliases'      => (isset($aliases) ? $aliases : array()),
      'group_suffix' => (isset($group_suffix) ? $group_suffix : ''),
      'default_uri'  => (isset($default_uri) ? $default_uri : 'http://localhost/{site}'),
    );

    return $custom;
  }
}

/**
 * Helper function to recursively merge arrays.
 */
if (!function_exists('array_merge_recursive_distinct')) {
  function array_merge_recursive_distinct(array &$array1, array &$array2) {
    $merged = $array1;

    foreach ($array2 as $key => &$value) {
      if (is_array($value) && isset($merged[$key]) && is_array($merged [$key] )) {
        $merged[$key] = array_merge_recursive_distinct($merged[$key], $value);
      }
      else {
        $merged[$key] = $value;
      }
    }

    return $merged;
  }
}

/**
 * For each entry, verify that it is a directory and then that it is a drupal
 * instance.
 */
foreach (scandir($web) as $root) {
  if (is_dir("$web/$root") && file_exists("$web/$root/sites/default/settings.php")) {

    // If this drupal root is delaring its own aliases and we are currently
    // working inside that root, don't add it to the global settings so the
    // local settings have the right of way.
    if (file_exists("$web/$root/sites/all/drush/aliases.drushrc.php") && stristr($cwd, "$web/$root")) {
      continue;
    }

    // Load any custom settings for this site if they are declared in the file
    // sites/all/drush/aliases.drushrc.inc
    $custom = _daconfig_get_settings("$web/$root/sites/all/drush/autoalias.drushrc.inc");

    // First, register multisite aliases.
    $sites = array();
    foreach (scandir("$web/$root/sites") as $site) {
      if (is_dir("$web/$root/sites/$site") && $site != 'default' && file_exists("$web/$root/sites/$site/settings.php")) {
        $alias = "{$root}.{$site}";
        $sites[$alias]['root'] = "$web/$root";
        $sites[$alias]['uri'] = str_replace('{site}', $site, $custom['default_uri']);
        $sites[$alias]['path-aliases']['%site'] = "$web/$root/sites/$site";
        $sites[$alias]['#group'] = array("{$root}{$custom['group_suffix']}");
      }
    }

    // If multisite aliases were found, create a grouped alias as the base.
    // Otherwise, alias the base.
    if (!empty($sites)) {
      // Add a default entry.  We do this here instead of allowing the default
      // dir when detecting multisites so single-site instances don't have
      // both a default and a group alias.
      $sites["{$root}.default"]['root'] = "$web/$root";
      $sites["{$root}.default"]['uri'] = str_replace('{site}', $root, $custom['default_uri']);
      $sites["{$root}.default"]['#group'] = array("{$root}{$custom['group_suffix']}");

      $auto_aliases += $sites;
    }
    // Create a monosite alias
    else {
      $auto_aliases[$root]['root'] = "$web/$root";
      $auto_aliases[$root]['uri'] = str_replace('{site}', $root, $custom['default_uri']);
    }

    // Merge with overrides
    if (!empty($custom['aliases'])) {
      $auto_aliases = array_merge_recursive_distinct($auto_aliases, $custom['aliases']);
    }
  }
}

// Create the groups
$groups = array();
foreach ($auto_aliases as $aa => $info) {
  if (is_array($info['#group'])) {
    foreach ($info['#group'] as $group) {
      $groups[$group]['site-list'][] = "@{$aa}";
    }
  }
}

// Merge any sourced aliases with our generated aliases.
$aliases += $auto_aliases += $groups;

autoalias.drushrc.inc

<?php
/**
 * @file
 * Drush aliases to be included into the global set.  To override these with
 * aliases that are only recognized within this Drupal root, place them into
 * sites/all/drush/aliases.drushrc.php.
 * 
 * Place this file in sites/all/drush/autoalias.drushrc.inc
 *
 * Override default auto-alias settings.
 *
 * $group_suffix = '';
 *   Add a common suffix to group multisite aliases.  Base is "ROOT"
 *
 *   Ex:
 *    $group_suffix = '.local';  would render the group alias as "ROOT.local"
 *
 * $default_uri;
 *   Define a custom uri pattern with the site name to generate the uri for each
 *   site.  Defaults to http://localhost/{site}
 *
 *   Ex:
 *    $default_uri = 'http://{site}.example.local'
 *
 * $aliases
 *   Define pieces of aliases and allow the auto-alias to fill in the rest.
 *   These settings will override anything that auto-alias may derrive.
 *
 *   Ex:
 *    $aliases['root.site'] = array(
 *      'uri' => 'http://different.uri.com,
 *      'path-aliases' => array(
 *        '%custom' => '/my/custom/path',
 *      ),
 *    );
 */
$group_suffix = '';
$default_uri  = '';
$aliases      = array();