Aardvark Topsites PHP
   A topsites script. [Open source, GPL]
   http://www.aardvarktopsitesphp.com/

FlexPHPLink
   A link management system allows to add, edit or delete links , easy internationalization, cheap customize service. [Freeware]
   http://www.china-on-site.com/flexphplink/

Free Directory Script
   Offers a free feature php based web directory script.
   http://www.freedirectoryscript.com/

GentleSource Link and Bookmark Manager
   Link manager can be used as link section of a website or a personal bookmark manager. You can publish links/bookmarks or hide them behind a login. [Free for private usage and non-profit organizations]
   http://www.gentlesource.com/link-manager/

Google API Search Script
   Free PHP script to search Google. Can be reistricted to search one site and language. Requires Google free license key. [Freeware]
   http://www.wwwsearchsolutions.com/google.php

InLink
   Commercial PHP portal-solution for running a Yahoo-style directory directly from a web site. Supports SQL, MySQL, PostgreSQL.
   http://www.in-portal.net/in-link/

Jade
   A PHP and MySQL based directory and search engine application that works with templates.
   http://www.jadetown.com/

Jax Link Lists
   An online hyperlink list manager for small link lists.
   http://www.jtr.de/scripting/php/linklists/index_eng.html

K-Links Directory
   Professional link indexing solution [Commercial]
   http://turn-k.net/k-links

K-Search
   Pay Per Click/MetaSearch script [Commercial]
   http://turn-k.net/k-search

Link Department
   Link management script with advanced yet easy to use admin control panel, fully template driven appearance, static HTML front-end and email notifications.
   http://hitcode.mywebftp.com/products/linkdept/

Link Up Gold
   Features unlimited categories and links, rating system, maillists, editor's pick, sponsors, and multiple languages.
   http://www.phpwebscripts.com/linkupgold/

LinksCaffePRO
   A mySQL/PHP4 portal solution that allows to run Yahoo-style directory.
   http://gonafish.com/index.php?id=1

Monster Top List
   Topsites script with webring, dynamic list position imaging, and RSS feeds. [Commercial]
   http://www.monstertoplist.com

OpenRealty
   A free, open source PHP real estate listing manager that uses a MySQL backend.
   http://jonroig.com/freecode/openrealty/

PHP Link Directory
   Software for running a link exchange or professional directory sorted by categories.
   http://www.phplinkdirectory.com/

PHPMini Links
   A link portal, which allows guests to add links as well. [Freeware]
   http://www.phpmini.com/downloads/links.php

PhpDig
   A search engine written in PHP that uses a MySQL database backend. It features indexing of both static and dynamic pages and full text indexing.
   http://www.phpdig.net/

ScriptRocket Top Site
   PHP Script for creating and run Top Sites. [Commercial]
   http://www.scriptrocket.com/tstopsite.php

ScriptsCenter.com
   A couple of commercial scripts, including AutoLinks+ and EzUpload.
   http://www.scriptscenter.com/

Site Search Pro
   A PHP fully-functional search engine for web site. Online demo. [Commercial]
   http://www.site-search-pro.com/

SkaLinks
   A link manager with links checking and advanced advertisement system. [Freeware]
   http://www.skalinks.com/

SmartPPC Search Engine
   Uses PHP and MySQL to keep advertiser/affiliate data, listings, full statistics, payment history, status, settings.
   http://www.orbitscripts.com/smartppc.html

Softbiz Automatic Link Checker
   Link validator tool written in PHP helps to check automatically if a page contain a link back to site. Helpful especially in link exchange or link popularity campaigns.
   http://www.softbizscripts.com/automatic-link-checker-script-features.php

Softbiz Link Directory Script
   Run own business link directory like dmoz. Customizable colors and graphics. Demo available.
   http://www.softbizscripts.com/link-directory-script-features.php

Softbiz Resource Repository Script
   Run own software repository site like hotscripts. Customizable colors and graphics. Demo available.
   http://www.softbizscripts.com/resource-repository-script-features.php

WSN Links
   A fully templated searchable links portal. Option to auto-notify admin of submissions and submitter of approval via email. Users may rate, email, report, and comment on each link. [Free with crediting text in footer, or commercial]
   http://scripts.webmastersite.net/wsnlinks/

X-Power Links
   A links management script with advanced, but easy to use admin control panel, fully template driven appearance, static HTML front-end. [Commercial]
   http://www.xpowerlinks.com/

aeDirectory
   A free PHP link directory script allows to build theme links directory.
   http://www.aewebworks.com/aedirectory.htm

eDirectory
   Application to manage online directories. Includes news, examples and FAQ.
   http://www.edirectory.com/

evoTopsites
   Advanced top site software that functions as a toplist, link directory, and/or webring. Built on top of PHP/MySQL and features dynamic hit tracking. [Freeware, req. registration]
   http://www.evo-dev.com/products/evotopsites/

iSearch
   A PHP/MySQL script for allowing visitors to a website to perform a search on the contents of the site. Includes multiple language support. [Free and Commercial]
   http://www.isearchthenet.com/isearch/

phpHoo
   A PHP script using MySQL that will display a "Yahoo-like" directory.
   http://www.cable-modems.org/phpHoo/

phpLinks
   A free link-farm, search engine PHP script that uses MySQL.
   http://sourceforge.net/projects/phplinks/

phpODP
   Add the content of The Open Directory Project to site. Let search, browse the categories. Also support for targeted advertising.
   http://www.bie.no/products/phpodp/

phpOpen
   Make a version of the Open Directory with this free PHP script.
   http://sourceforge.net/projects/phpopen/phpOpen/

phpYellow Pages
   A generic directory builder to create free or paid directory [Free and commercial versions]
   http://phpyellow.com/