The navigation at the bottom of my site (http://agabus.com) does not work on the index page -- it does work on the search page. I think the problem rests with the them, for the navigation works on other themes. Here is the code for the theme in question; I'm using the "Journalist" theme featured at WordPress.
<?php get_header(); ?>
<?php
if (is_home()) {
query_posts("cat=-29");
}
?>
<div id="content" class="group">
<?php if (have_posts()) : while (have_posts()) : the_post(); ?>
<h2 id="post-<?php the_ID(); ?>"><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h2>
<p class="comments"><a href="<?php comments_link(); ?>"><?php comments_number('comments','with one comment','with % comments'); ?></a></p>
<div class="main">
<?php the_content('Read the rest of this entry »'); ?>
</div>
<div class="meta group">
<div class="signature">
<p>Written by <?php the_author() ?> <span class="edit"><?php edit_post_link('Edit'); ?></span></p>
<p><?php the_time('F jS, Y'); ?> <?php _e("at"); ?> <?php the_time('g:i a'); ?></p>
</div>
<div class="tags">
<p><?php if(function_exists('wp_email')) { email_link(); } ?></p>
<p><?php if(function_exists('wp_print')) { print_link(); } ?></p>
</div>
</div>
<?php if ( comments_open() ) comments_template(); ?>
<?php endwhile; else: ?>
<div class="warning">
<p>Sorry, but you are looking for something that isn't here.</p>
</div>
<?php endif; ?>
<div class="navigation">
<div class="alignleft"><?php next_posts_link('« Older Entries') ?></div>
<div class="alignright"><?php previous_posts_link('Newer Entries »') ?></div>
</div>
</div>
<?php get_sidebar(); ?>
<?php get_footer(); ?>