You can disable the Compare products functionality by following the steps listed below:

1. Edit app/code/core/Mage/Catalog/Helper/Product/Compare.php and change the following code:

public function getAddUrl($product)
{
return $this->_getUrl(’catalog/product_compare/add’, $this->_getUrlParams($product));
}

to:

public function getAddUrl($product)
{
//return $this->_getUrl(’catalog/product_compare/add’, $this->_getUrlParams($product));
return false;
}

2. Edit ./app/design/frontend/base/default/layout/catalog.xml (if you are using a different Magento theme, enter its name instead of default) and change the following code:

<block type="catalog/product_compare_sidebar" before="cart_sidebar" name="catalog.compare.sidebar" template="catalog/product/compare/sidebar.phtml"/>

to:

<!-- <block type="catalog/product_compare_sidebar" before="cart_sidebar" name="catalog.compare.sidebar" template="catalog/product/compare/sidebar.phtml"/> -->

3. Flush the Magento cache from your Magento admin area->System->Cache Management.