Trouble with Multiple Loop and Pagination

I’m trying to design a site just like GigaOm, where the homepage displays a Feature story, three featured headlines, then the standard Loop (which excludes that Featured category). In other words, like this.

What I tried so far seems to work, but when I click “Older Posts”, it just reprints the same posts without excluding newer ones:

<!--MAIN FEATURED-->
<?php query_posts('showposts=1&cat=5'); ?>
<?php while (have_posts()) : the_post(); ?>
<h2><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h2>

<div class="entry">
<?php the_content('<br /><span>&raquo;Read More</span>'); ?>
</div>
<?php endwhile; ?>

<!--THREE FEATURED HEADLINES-->
<?php query_posts('showposts=3&offset=1&cat=5'); ?>
<ul>
<?php while (have_posts()) : the_post(); ?>
<li><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></li>
<?php endwhile; ?>
</ul>

<!--STANDARD LOOP-->
<?php query_posts('cat=-5'); ?>
<?php if (have_posts()) : ?>

 <?php while (have_posts()) : the_post(); ?>
   <div class="post" id="post-<?php the_ID(); ?>">
				<h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
				<p class="postmetadata">Posted by <?php the_author_posts_link(); ?> on <?php the_time('F jS, Y') ?>
				<span class="commentcount"><?php comments_popup_link('No Comments »', '1 Comment »', '% Comments »'); ?></span></p>

				<div class="entry clearfloat">
					<?php the_content('<br /><span>&raquo;Read More</span>'); ?>
				</div>
			</div>

 <?php endwhile; ?>
	<div class="navigation">
			<div class="alignleft"><?php next_posts_link('&laquo; Older Entries') ?></div>
			<div class="alignright"><?php previous_posts_link('Newer Entries &raquo;') ?></div>
		</div>

	<?php else : ?>

		<h2 class="center">Not Found</h2>
		<p class="center">Sorry, but you are looking for something that isn't here.</p>
		<?php include (TEMPLATEPATH . "/searchform.php"); ?>

	<?php endif; ?>

I also noticed that on GigaOm, when you view /page/2/, the Featured box goes away. How is this done, since they’re both using the “index.php” template? I tried a “if is_home” conditional, but it didn’t work.

Thanks!