gistfile1.php

<?php
include 'app/Mage.php';
Mage::app();
$file = fopen("skus.csv", "r");
while ($data = fgetcsv($file, 1000, ",")) {
    $old = $data[0];
    $new = $data[1];
    $product = Mage::getModel('catalog/product')->loadByAttribute('sku', $old);
    if($product && $product->getId()){
        $product->setSku($new);
        $product->save();
    }
}
fclose($file);