Show WP Popular Posts without plugin.

functions.php

<?php
// Add this in your functions file
function count_post_visits() {
    if( is_single() ) {
        global $post;
        $views = get_post_meta( $post->ID, 'my_post_viewed', true );
        if( $views == '' ) {
            update_post_meta( $post->ID, 'my_post_viewed', '1' );   
        } else {
            $views_no = intval( $views );
            update_post_meta( $post->ID, 'my_post_viewed', ++$views_no );
        }
    }
}
add_action( 'wp_head', 'count_post_visits' );

template-file.php

<?php
//Paste the following wherever in your template files that you wish to display the popular posts
$popular_posts_args = array(
    'posts_per_page' => 3,
    'meta_key' => 'my_post_viewed',
    'orderby' => 'meta_value_num',
    'order'=> 'DESC'
);
$popular_posts_loop = new WP_Query( $popular_posts_args );
  while( $popular_posts_loop->have_posts() ):
    $popular_posts_loop->the_post();
    // Loop continues
endwhile;
wp_reset_query();