Edit your theme's "templae/catalog/product/view/addto.phtml" file. Find and Comment the below lines.
<?php
$_compareUrl = $this->helper('catalog/product_compare')->getAddUrl($_product);
?>
<?php if($_compareUrl) : ?>
<li><span class="separator">|</span> <a href="<?php echo $_compareUrl ?>" class="link-compare"><?php echo $this->__('Add to Compare') ?></a></li>
<?php endif; ?>
