Example of importing skus and changing attribute sets.

changeAttributeSetImport.php

<?php
/**
* changeAttributeSetImport.php
* Allows you to change the attribute set for a list of skus
*
* @author      Tegan Snyder <tsnyder@mmm.com>
*/

/* 
Preparing your file:
There are two ways to change attribute sets for a list of skus.

Option #1:
Setup a CSV file with the following column headers:
"sku","attribute_set_id"

Option #2:
Setup a CSV file with the following column headers:
"sku","attribute_set_name"
*/

$filename = 'skus.csv';

require_once('app/Mage.php');
umask(0);
Mage::app();

$store_id = 0;

// load CSV to associative array
$csv = array();
if(($handle = fopen($filename, "r")) !== FALSE) {
  $rowCounter = 0;
  while (($rowData = fgetcsv($handle, 0, ",")) !== FALSE) {
    if (0 === $rowCounter) {
      $headerRecord = $rowData;
    } else {
      foreach( $rowData as $key => $value) {
        $csv[$rowCounter - 1][$headerRecord[$key]] = $value;
      }
    }
    $rowCounter++;
  }
  fclose($handle);
}

$cnt = 0;

// store product ids we change attribute sets on here
$product_ids_changed = array();

foreach ($csv as $row) {

  $model = Mage::getModel('catalog/product');

  if (!isset($row['sku'])) {
    echo '#' . $cnt . ' sku not found: ' . PHP_EOL;
    $cnt = $cnt + 1;
    continue;
  }

  $product_id = $model->getIdBySku($row['sku']);

  if (isset($row['attribute_set_id'])) {

    $attribute_set_id = $row['attribute_set_id'];

  } elseif (isset($row['attribute_set_name'])) {

    $attribute_set_name = $row['attribute_set_name'];

    $attribute_set_id = Mage::getModel('eav/entity_attribute_set')
      ->load($attribute_set_name, 'attribute_set_name')
      ->getAttributeSetId();

  } else {
    echo '#' . $cnt . ' no identifier found (use attribute_set_id or attribute_set_name): ' . $row['sku'] . PHP_EOL;
    $cnt = $cnt + 1;
    continue;
  }

  if (empty($attribute_set_id)) {
    echo '#' . $cnt . ' empty: ' . $row['sku'] . PHP_EOL;
    $cnt = $cnt + 1;
    continue;
  }

  try {

    $product = Mage::getModel('catalog/product')->setStoreId($store_id)->load($product_id);
    $product->setAttributeSetId($attribute_set_id)->setStoreId($store_id);
    $product->save();

    $product_ids_changed[$cnt] = $product_id;

    echo '#' . $cnt . ' success: ' . $row['sku'] . PHP_EOL;

  } catch (Exception $e) {

/* 
  If you get an error like this:

  Product with the 'scotch-light-duty-packaging-tape-610-clear-heat-resistant-1-2-in-x-72-yd-70006788395' url_key attribute already exists.

  when changing attribute sets take a look here:
  app/code/core/Enterprise/Catalog/Model/Product/Attribute/Backend/Urlkey.php

  The store id of the the query Magento runs against:

  SELECT `catalog_product_entity_url_key`.`entity_id`, 
  `catalog_product_entity_url_key`.`store_id` 
  FROM `catalog_product_entity_url_key` 
  WHERE (value = 'scotch-light-duty-packaging-tape-610-clear-heat-resistant-1-2-in-x-72-yd-70006788395') LIMIT 1

  Returns a store_id row and if the store_id row doesn't match the $store_id variable above you will get that error

  $row['store_id'] == $object->getStoreId() on the object

*/

    echo '#' . $cnt . ' error: ' . $row['sku'] . PHP_EOL;
    echo $e->getMessage() . PHP_EOL;
  }

  $cnt = $cnt + 1;

}

if ($cnt == 0) {

  echo 'No records found in file';

} else {

  Mage::dispatchEvent('catalog_product_massupdate_after', array('products' => $product_ids_changed));

}

run this over bash prompt:

php changeAttributeSetImport.php

Thanks Tegan - as per our chat - just needs a slight tweak :-

The comment in line 13 should read :-

// prepare a file called skus.csv with sku, attribute_set
// attribute_set refers to the NAME of the attribute set

@BFG9000 I updated it