Particle Links allows you to easy setup a links directory. Complete with an installer, all you have to do is enter a few details such as the site's name and user details to get started.
In the directory you can create unlimited layers of topics and sub-topics and unlimited websites under each. Users can then browse the topics (support for static URLs is available) or use the search function (full text search supported) to find the websites they are looking for.
There is also an admin panel to update the site's configuration, a skin editor where you can change the look and feel of the site (supports multiple skins which users can choose between) and a moderation panel where you can create and edit the topics and websites.
Users can also submit websites (which you can enable and disable) and these are placed in the moderation queue so that you can either accept or reject them before they are added to the directory.
