How to get thumbnail from post attachment in this loop

If I understand your question correctly, you want to retrieve the first attached image to each post & use the thumbnail size, rather than parsing the content for embedded images & using timthumb?

If so, set your thumbnail size to the required size (60×60) in the media options page, make sure you’ve drag n dropped the attachments into the required order, then use the following code (note that I’m not a fan of query_posts, I much prefer using get_posts).

$args = array(
        'meta_key'       => 'views',
        'orderby'        => 'meta_value_num',
        'order'          => 'DESC',
        'posts_per_page' => 9
    );

$popular_posts = get_posts( $args );

if ( $popular_posts ) {

    echo '<h2>Popular Posts</h2>';
    echo '<ul>';

    foreach ( $popular_posts as $popular_post ) {

        $kids_args = array(
                'post_parent'    => $popular_post->ID,
                'post_type'      => 'attachment',
                'post_status'    => null,
                'post_mime_type' => 'image',
                'orderby'        => 'menu_order',
                'order'          => 'ASC',
                'posts_per_page' => 1
                );

        $kids = get_posts( $kids_args );

        echo '<li>';
        if ( $kids ) {
            foreach ( $kids as $kid ) {
                $img = wp_get_attachment_image_src( $kid->ID );
                printf( '<a href="https://wordpress.stackexchange.com/questions/47354/%s" title="https://wordpress.stackexchange.com/questions/47354/%s"><img src="https://wordpress.stackexchange.com/questions/47354/%s" width="https://wordpress.stackexchange.com/questions/47354/%s" height="https://wordpress.stackexchange.com/questions/47354/%s"></a>',
                    get_permalink( $popular_post->ID ),
                    esc_attr( get_the_title( $popular_post->ID ) ),
                    $img[0],
                    $img[1],
                    $img[2]
                    );
            }
        } else {
            printf( '<a href="https://wordpress.stackexchange.com/questions/47354/%s" title="https://wordpress.stackexchange.com/questions/47354/%s"><img src="https://wordpress.stackexchange.com/questions/47354/%s" width="https://wordpress.stackexchange.com/questions/47354/%s" height="https://wordpress.stackexchange.com/questions/47354/%s"></a>',
                get_permalink( $popular_post->ID ),
                esc_attr( get_the_title( $popular_post->ID ) ),
                get_bloginfo( 'template_url' ) . '/images/default.jpg',
                60,
                60
                );
        }
        echo '</li>';

    }

    echo '</ul>';

}

I’m writing from memory, not in a position to test it now, so hopefully it works!