you can use <?=$website_url?>
in the portfolio template like
<strong>URL: </strong><a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?=$website_url?></a>
to make it like follow
<?php
/*
Template Name: Portfolio
*/
?>
<?php get_header(); ?>
<div id="content">
<?php
$loop = new WP_Query(array('post_type' => 'portfolio', 'posts_per_page' => 10));
?>
<?php while ( $loop->have_posts() ) : $loop->the_post(); ?>
<?php
$custom = get_post_custom($post->ID);
$screenshot_url = $custom["screenshot_url"][0];
$website_url = $custom["website_url"][0];
?>
<div id="portfolio-item">
<h1><?php the_title(); ?></h1>
<a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?php the_post_thumbnail(); ?> </a>
<strong>URL: </strong><a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?=$website_url?></a>
<?php the_content(); ?>
</div>
<?php endwhile; ?>
</div><!-- #content -->
<?php get_footer(); ?>
You can change the placement to match your standers