This small script looks for products with a higher special price than normal price and removes the special price if the $emptySpecialPrice flag is set to true. Be sure to reindex the prices after running this.

checkPricesVsSpecialPrice.php

<?php

chdir(dirname(__FILE__));

require_once '../app/Mage.php';
Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID);
umask(0);

$resource = Mage::getModel('core/resource');
$db = $resource->getConnection('core_write');

$specialPriceAttributeId = $db->fetchOne($db->select()->from('eav_attribute')->where('attribute_code = ?', 'special_price')->where('entity_type_id = ?', 4));

$products = Mage::getModel('catalog/product')->getCollection()->addAttributeToSelect(array('name','price'))->addFieldToFilter('special_price', array('neq'=>''));

$emptySpecialPrice = false;

echo "Name\tSKU\tPrice\tSpecialPrice\n";
foreach($products as $product) {
    if($product->getPrice() <= $product->getSpecialPrice()) {
        echo $product->getName() . "\t" . $product->getSku() . "\t" . $product->getPrice() . "\t" . $product->getSpecialPrice() . "\n";
        if($emptySpecialPrice) {
            $db->delete('catalog_product_entity_decimal', 'attribute_id = ' . $specialPriceAttributeId . ' AND entity_id = ' . $product->getId());
            echo 'Special price for ' . $product->getSku() . ' has been deleted.' . PHP_EOL;
        }
    }
}