I\'ve imported 6K categories and 16K products to magento using a custom import profile. When I\'m trying to reindex everything works except for \'Catalog URL Rewrites\' that kee
My own attempt of reindexing URL rewrites was with 10,000 products and it took me like an Hour and Half to finish up.
this link will help you do it from Command Line , which is preferable than doing it from the same Magento admin panel.
http://www.yireo.com/tutorials/magento/magento-administration/340-magento-14-cronjobs
Make sure you read the part about skipping some basic configuration when facing memory limits , this is the one i usually use.