The two options I use are Drush and a custom script.

For Drush, you can use drush pm-list

$ drush help pm-list
Show a list of available extensions (modules and themes).

Options:
 --type                                    Filter by extension type. Choices:
                                           module, theme.
 --status                                  Filter by extension status. Choices:
                                           enabled, disable and/or 'not
                                           installed'. You can use multiple
                                           comma separated values. (i.e.
                                           --status="disabled,not installed").
 --package                                 Filter by project packages. You can
                                           use multiple comma separated values.
                                           (i.e. --package="Core -
                                           required,Other").
 --core                                    Filter out extensions that are not
                                           in drupal core.
 --no-core                                 Filter out extensions that are
                                           provided by drupal core.
 --pipe                                    Returns a space delimited list of
                                           the names of the resulting
                                           extensions.


Aliases: pml

I also wrote this script for Drupal 6. You need to edit the bootstrap for Drupal 7, and you may also want to tweak the path checking. I put this in a file called modules.php in my DOCROOT and add access restriction around it to prevent it from being called from the wild.

<?php
include_once './includes/bootstrap.inc';
drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
header('Content-Type: text/plain');

$files = drupal_system_listing('\.module$', 'modules', 'name', 0);

system_get_files_database($files, 'module');

ksort($files);

$core_installed = array();
$core_enabled = array();
$core_disabled = array();

$contrib_installed = array();
$contrib_enabled = array();
$contrib_disabled = array();

foreach ($files as $info) {
  $filename = $info->filename;
  $name = $info->name;
  $status = $info->status;
  
  $contrib = strpos($filename, "sites/all/modules/") === 0;
  
  if ($contrib) {
    $contrib_installed[] = $name;
    if ($status) $contrib_enabled[] = $name;
    else $contrib_disabled[] = $name;
  } else {
    $core_installed[] = $name;
    if ($status) $core_enabled[] = $name;
    else $core_disabled[] = $name;
  }
}

print "Installed Core Modules: " . join(", ", $core_installed) . "\n\n";
print "Enabled Core Modules: " . join(", ", $core_enabled) . "\n\n";
print "Disabled Core Modules: " . join(", ", $core_disabled) . "\n\n";

print "Installed Contrib Modules: " . join(", ", $contrib_installed) . "\n\n";
print "Enabled Contrib Modules: " . join(", ", $contrib_enabled) . "\n\n";
print "Disabled Contrib Modules: " . join(", ", $contrib_disabled) . "\n\n";