<?php
    
    $comments = array(
        array(
            'id' => 1,
            'parent_id' => 0,
            'body' => 'Some comment',
            'created' => 123456798,
        ),
        array(
            'id' => 2,
            'parent_id' => 0,
            'body' => 'Some comment',
            'created' => 123456798,
        ),
        array(
            'id' => 3,
            'parent_id' => 0,
            'body' => 'Some comment',
            'created' => 123456798,
        ),
        array(
            'id' => 4,
            'parent_id' => 0,
            'body' => 'Some comment',
            'created' => 123456798,
        ),
        array(
            'id' => 5,
            'parent_id' => 2,
            'body' => 'Some comment',
            'created' => 123456798,
        ),
        array(
            'id' => 6,
            'parent_id' => 2,
            'body' => 'Some comment',
            'created' => 123456798,
        ),

    );

    
    $thread = array();
    $comment_refs = array();
    foreach($comments as $comment){
        $parent_id = $comment['parent_id'];
        $comment_id = $comment['id'];

        if (!isset($comment_refs[$parent_id])) {
            // No parent comment so just add it to the thread
            $thread[] = $comment;
            $tmp_key = count($thread) - 1;
            
            // Add a replies element to hold any future replies
            $thread[$tmp_key]['replies'] = array();

            // Make a reference to this comment so we can find it later
            $comment_refs[$comment_id] = &$thread[count($thread)-1];

        } else {
            // Parent comment available, so add it there
            $comment_refs[$parent_id]['replies'][] = $comment;
            
            // Make a reference to this comment so we can find it later
            $replies = &$comment_refs[$parent_id]['replies'];
            $comment_refs[$comment_id] = &$replies[count($replies)-1];
        }
    }

    unset($comment_refs);
    print_r($thread);