How to add comment numbering to a WordPress theme using Greg's Threaded Comment Numbering plugin. Includes support for Genesis.

gregs-threaded-comment-numbering-gnesis.css

/* Greg's Threaded Comment Numbering Genesis
--------------------------------------------- */
.commentnumber {
	display: block;
	float: right;
	font-size: 40px;
	font-size: 4rem;
	margin-left: 20px;
	margin-left: 2rem;
	padding: 0 20px;
	padding: 0 2rem;
}

gregs-threaded-comment-numbering-gnesis.php

<?php

add_filter( 'genesis_comment_list_args', 'prefix_numbered_comment_filter' );
/**
 * Integrate Greg's Threaded Comment Numbering plugin by overriding
 * the default Genesis comment callback function.
 *
 * @param     $args Default genesis comment args.
 * @return    $args Modifed comment args with new callback function.
 * 
 * @copyright Copyright (c) 2014, FAT Media, LLC
 */
function prefix_numbered_comment_filter( $args ) {
	if ( ! function_exists( 'gtcn_comment_numbering' ) ) {
		return $args;
	}
	$args['callback'] = 'prefix_numbered_comment_callback';
	return $args;
}

/**
 * Comment callback for {@link genesis_default_list_comments()} if HTML5 is active.
 *
 * Does `genesis_before_comment` and `genesis_after_comment` actions.
 *
 * Applies `comment_author_says_text` and `genesis_comment_awaiting_moderation` filters.
 *
 * @since 2.0.0
 *
 * @param stdClass $comment Comment object.
 * @param array    $args    Comment args.
 * @param integer  $depth   Depth of current comment.
 */
function prefix_numbered_comment_callback( $comment, array $args, $depth ) {

	$GLOBALS['comment'] = $comment; ?>

	<li <?php comment_class(); ?> id="comment-<?php comment_ID(); ?>">
	<article <?php echo genesis_attr( 'comment' ); ?>>

		<?php do_action( 'genesis_before_comment' ); ?>
		<?php echo gtcn_comment_numbering( $comment->comment_ID, $args ); ?>

		<header class="comment-header">
			<p <?php echo genesis_attr( 'comment-author' ); ?>>
				<?php
				echo get_avatar( $comment, $args['avatar_size'] );

				$author = get_comment_author();
				$url    = get_comment_author_url();

				if ( ! empty( $url ) && 'http://' !== $url ) {
					$author = sprintf( '<a href="%s" rel="external nofollow" itemprop="url">%s</a>', esc_url( $url ), $author );
				}

				printf( '<span itemprop="name">%s</span> <span class="says">%s</span>', $author, apply_filters( 'comment_author_says_text', __( 'says', 'theme-textdomain' ) ) );
				?>
		 	</p>

			<p class="comment-meta">
				<?php
				$pattern = '<time itemprop="commentTime" datetime="%s"><a href="%s" itemprop="url">%s %s %s</a></time>';
				printf( $pattern, esc_attr( get_comment_time( 'c' ) ), esc_url( get_comment_link( $comment->comment_ID ) ), esc_html( get_comment_date() ), __( 'at', 'theme-textdomain' ), esc_html( get_comment_time() ) );

				edit_comment_link( __( '(Edit)', 'theme-textdomain' ), ' ' );
				?>
			</p>
		</header>

		<div class="comment-content" itemprop="commentText">
			<?php if ( ! $comment->comment_approved ) : ?>
				<p class="alert"><?php echo apply_filters( 'genesis_comment_awaiting_moderation', __( 'Your comment is awaiting moderation.', 'theme-textdomain' ) ); ?></p>
			<?php endif; ?>

			<?php comment_text(); ?>
		</div>

		<?php
		comment_reply_link( array_merge( $args, array(
			'depth'  => $depth,
			'before' => '<div class="comment-reply">',
			'after'  => '</div>',
		) ) );
		?>

		<?php do_action( 'genesis_after_comment' ); ?>

	</article>
	<?php
	//* No ending </li> tag because of comment threading
}

gregs-threaded-comment-numbering-twentyfourteen.php

<?php
/**
 * The template for displaying Comments
 *
 * The area of the page that contains comments and the comment form.
 *
 * @package WordPress
 * @subpackage Twenty_Fourteen
 * @since Twenty Fourteen 1.0
 */

/*
 * If the current post is protected by a password and the visitor has not yet
 * entered the password we will return early without loading the comments.
 */
if ( post_password_required() ) {
	return;
}
?>

<div id="comments" class="comments-area">

	<?php if ( have_comments() ) : ?>

	<h2 class="comments-title">
		<?php
			printf( _n( 'One thought on &ldquo;%2$s&rdquo;', '%1$s thoughts on &ldquo;%2$s&rdquo;', get_comments_number(), 'twentyfourteen' ),
				number_format_i18n( get_comments_number() ), get_the_title() );
		?>
	</h2>

	<?php if ( get_comment_pages_count() > 1 && get_option( 'page_comments' ) ) : ?>
	<nav id="comment-nav-above" class="navigation comment-navigation" role="navigation">
		<h1 class="screen-reader-text"><?php _e( 'Comment navigation', 'twentyfourteen' ); ?></h1>
		<div class="nav-previous"><?php previous_comments_link( __( '&larr; Older Comments', 'twentyfourteen' ) ); ?></div>
		<div class="nav-next"><?php next_comments_link( __( 'Newer Comments &rarr;', 'twentyfourteen' ) ); ?></div>
	</nav><!-- #comment-nav-above -->
	<?php endif; // Check for comment navigation. ?>

	<ol class="comment-list">
	<?php
		$callback = null;
		if ( function_exists('gtcn_basic_callback') ) {
			$callback = 'gtcn_basic_callback';
		}
		wp_list_comments( array(
			'style'      => 'ol',
			'short_ping' => true,
			'avatar_size'=> 34,
			'callback'   => $callback,
		) );
	?>
	</ol><!-- .comment-list -->

	<?php if ( get_comment_pages_count() > 1 && get_option( 'page_comments' ) ) : ?>
	<nav id="comment-nav-below" class="navigation comment-navigation" role="navigation">
		<h1 class="screen-reader-text"><?php _e( 'Comment navigation', 'twentyfourteen' ); ?></h1>
		<div class="nav-previous"><?php previous_comments_link( __( '&larr; Older Comments', 'twentyfourteen' ) ); ?></div>
		<div class="nav-next"><?php next_comments_link( __( 'Newer Comments &rarr;', 'twentyfourteen' ) ); ?></div>
	</nav><!-- #comment-nav-below -->
	<?php endif; // Check for comment navigation. ?>

	<?php if ( ! comments_open() ) : ?>
	<p class="no-comments"><?php _e( 'Comments are closed.', 'twentyfourteen' ); ?></p>
	<?php endif; ?>

	<?php endif; // have_comments() ?>

	<?php comment_form(); ?>

</div><!-- #comments -->

gregs-threaded-comment-numbering.css

/* Greg's Threaded Comment Numbering
--------------------------------------------- */
.commentnumber {
	display: block;
	float: right;
	font-size: 40px;
	margin-left: 20px;
	padding: 0 20px;
}

twentyfourteen-comments.php

<?php
/**
 * The template for displaying Comments
 *
 * The area of the page that contains comments and the comment form.
 *
 * @package WordPress
 * @subpackage Twenty_Fourteen
 * @since Twenty Fourteen 1.0
 */

/*
 * If the current post is protected by a password and the visitor has not yet
 * entered the password we will return early without loading the comments.
 */
if ( post_password_required() ) {
	return;
}
?>

<div id="comments" class="comments-area">

	<?php if ( have_comments() ) : ?>

	<h2 class="comments-title">
		<?php
			printf( _n( 'One thought on &ldquo;%2$s&rdquo;', '%1$s thoughts on &ldquo;%2$s&rdquo;', get_comments_number(), 'twentyfourteen' ),
				number_format_i18n( get_comments_number() ), get_the_title() );
		?>
	</h2>

	<?php if ( get_comment_pages_count() > 1 && get_option( 'page_comments' ) ) : ?>
	<nav id="comment-nav-above" class="navigation comment-navigation" role="navigation">
		<h1 class="screen-reader-text"><?php _e( 'Comment navigation', 'twentyfourteen' ); ?></h1>
		<div class="nav-previous"><?php previous_comments_link( __( '&larr; Older Comments', 'twentyfourteen' ) ); ?></div>
		<div class="nav-next"><?php next_comments_link( __( 'Newer Comments &rarr;', 'twentyfourteen' ) ); ?></div>
	</nav><!-- #comment-nav-above -->
	<?php endif; // Check for comment navigation. ?>

	<ol class="comment-list">
		<?php
			wp_list_comments( array(
				'style'      => 'ol',
				'short_ping' => true,
				'avatar_size'=> 34,
			) );
		?>
	</ol><!-- .comment-list -->

	<?php if ( get_comment_pages_count() > 1 && get_option( 'page_comments' ) ) : ?>
	<nav id="comment-nav-below" class="navigation comment-navigation" role="navigation">
		<h1 class="screen-reader-text"><?php _e( 'Comment navigation', 'twentyfourteen' ); ?></h1>
		<div class="nav-previous"><?php previous_comments_link( __( '&larr; Older Comments', 'twentyfourteen' ) ); ?></div>
		<div class="nav-next"><?php next_comments_link( __( 'Newer Comments &rarr;', 'twentyfourteen' ) ); ?></div>
	</nav><!-- #comment-nav-below -->
	<?php endif; // Check for comment navigation. ?>

	<?php if ( ! comments_open() ) : ?>
	<p class="no-comments"><?php _e( 'Comments are closed.', 'twentyfourteen' ); ?></p>
	<?php endif; ?>

	<?php endif; // have_comments() ?>

	<?php comment_form(); ?>

</div><!-- #comments -->

We've also posted a tutorial explaining this code as well as a full review of Greg's Threaded Comment Numbering over on WP Bacon.