Snippet to add a smarter option to Mandrill for WordPress.

functions.php

<?php 

/**
 * Add paragraph breaks to plain text notifications sent by Mandrill
 *
 * Mandrill's default option for handling this is a bit too
 * agressive. This method checks the type of email, and attempts
 * to detect whether or not it is HTML or not.
 *
 * @param  array $message
 * @return array Modified $message
 */
function wpmandrill_auto_add_breaks($message) {
  $html = $message['html'];

  $is_comment_notification = ( $message['tags']['automatic'][0] == 'wp_wp_notify_moderator' );
  $is_password_reset = ( $message['tags']['automatic'][0] == 'wp_retrieve_password' );
  $no_html_found = ( $html == strip_tags($html) );

  // Add line breaks and links to messages that don't appear to be HTML
  if ( $no_html_found || $is_comment_notification || $is_password_reset ) {
    $html = wpautop($html);
    $message['html'] = make_clickable($html);
  }
  return $message;
}
add_filter('mandrill_payload', 'wpmandrill_auto_add_breaks');