PHP Link Directory

A very popular script with thousands of directories using both the free and the paid versions. From the looks of it, this directory script is pretty well maintained with new versions coming out every few months. Their forums are very active as well with their support staff being there. You will also find free (and paid) third party modifications in the forum.
This script allows users to change their template easily and comes with a ton of features, like SE friendly URLs, payment system integrated, IP and Domain banning, link details page, RSS feed and many more. The latest version adds an article submission option to PhpLD.
Features Live Demo