Hi,

I have a filter set up got wp_make_link_relative to remove the site url from most of the links.

Surprisingly the new version of Disqus released a few days ago ended up having an error on my site which was caused be the relative url in disqus_url variable.

To avoid this, I added a very ugly quick-fix to the plugin:
comments.php, line #46

-    var disqus_url = '<?php echp get_permalink();'?>
+    var disqus_url = '<?php $plink = get_permalink(); $url = get_bloginfo('url'); if ( !strstr( $url, $plink ) ) $plink = $url . $plink; echo $plink; ?>';

The filter code I’m using in functions.php:

$this->urlfilters = array(
                'post_link',
                'post_type_link',
                'page_link',
                'attachment_link',
                'post_type_archive_link',
                'get_pagenum_link',
                'get_comments_pagenum_link',
                'term_link',
                'search_link',
                'day_link',
                'month_link',
                'year_link',
                'option_siteurl',
                'blog_option_siteurl',
                'option_home',
                'admin_url',
                'home_url',
                'includes_url',
                'site_url',
                'site_option_siteurl',
                'get_the_author_url',
                'get_comment_link',
                'wp_get_attachment_image_src',
                'wp_get_attachment_thumb_url',
                'wp_get_attachment_url',
                'wp_login_url',
                'wp_logout_url',
                'wp_lostpassword_url',
            );

            if ( ! is_feed()  && ! get_query_var( 'sitemap' ) ) {
                foreach ( $this->urlfilters as $filter ) {
                    add_filter( $filter, 'wp_make_link_relative' );
                }
            }

I know this is a rare case but it might affect others as well in the future.

http://wordpress.org/plugins/disqus-comment-system/