Has both free and $50 versions. Outbound links by default go through a redirect (not spiderable links) counts traffic. The software also has a built in link checker.
http://www.hitcode.com/products/linkdept/
Offers a free version if you leave the tag line. Two other versions cost $50 or $700. This site is powered by the $50 version of this script.
http://www.directory-search.org/directory_script.php
Prices range from $150 to $450. Offers both links 2.0, and links SQL.
http://www.gossamer-threads.com/
Free script good for making smaller direcories. If you have an exceptionally large idea it would be a bad script to use, but a great script for smaller sites.
http://www.cable-modems.org/phphoo/
WSN Links has a one time license fee of $35 to run up to three coppies of it's directory script at different locations.
http://www.wsnlinks.com/
(free or $20) This script has many cool features and allows you to even rate things which do not even have a URL.
http://scripts.dbmasters.net/index.php?n=42&id=40
free script based on php & MySQL. Can provide a static or dynamic directory.
http://scripts.digitalmakers.com/dmjade.php
Directory script that builds search engines friendly, static pages. Main idea is to build effective structure to maximize directory traffic potential, heavy optimization and heavy traffic volumes.
http://www.aewebworks.com/aedirectory.htm
$399 with free install. One of the better directory scripts available.
http://www.focalmedia.net/pseek.html
Links indexing directory for presenting visitors with an organised heirarchy of links. Static and non-static versions available. Costs a one time $50 fee.
http://www.bosdev.com/bosdirectory/