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Link Indexing 
1. MyThreads-Links
MyThreads-Links is a flexible web based links manager that looks similar to Yahoo but was written in PHP and uses MySQL. MyThreads-Links uses PHPLib Templates so that its very simple for anyone to change the look and feel of the program without having to edit the code.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: Platform Independent
2. Skalinks Links Management Script
SkaLinks was created for arranging link categories with use of reciprocal links exchange concept. Features: links exchange; categories hierarchy; virtual categories; related categories; admin panel; customizable settings; statistics display; broken links verification; fast-to-customize interface.
Development Status: Not Available
License: Other/Proprietary License
Operating System: Linux/Unix, Windows
3. Yet Another Link Directory
Yet another link directory (YALD) is a simple yet powerful and efficient link directory/index program written in PHP with a MySQL backend. YALD also features easily customizable templates and unlimited subcategories.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: All 32-bit MS Windows (95/98/NT/2000/XP), All POSIX (Linux/BSD/UNIX-like OSes)
4. Plugboard
Plugboard is a small and simple script that allows users to post a button link on your site. Features include IP logging, domain banning, IP banning, set image size, flood control and no double plugs. Keep your visitors coming back.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: Windows, Linux
5. OpenLD
OpenLD is an open and free link-directory. Some features are: SEO-friendly urls, a plugin engine and an easy install.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: OS Independent (Written in an interpreted language)
6. qlWebDS - Web Directory Software
qlWebDS Web Directory Script offers unique tools and features. Deep links, banner rotator, ad placement right through admin, 5 languages, meta fetch, instant sub-category creation, 9 link choices, 11 templates, optional auto approvals, free and paid premium version. Written in PHP for MySQL.
Development Status: Mature
License: GNU General Public License (GPL)
Operating System: linux, windows, freebsd, osx, sun
7. phpLinkDirectory Free Directory Script
Create a general directory of the best resources accross the web, and allow people to submit their sites. You can also earn money by charging for the review process, as well as a premium for featured links. Many have profitted from this model, and people continue to do this today.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: Unix, Win
8. PHP Weby directory script
Free directory script to create your own catelog of listings, directory of links, dmoz, or yahoo style directory. Features include: unlimited categories and subcategories, link checker, link editor, SEO urls, paypal integration, template driven system and more.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: ALL
9. Link Base 2.0.
This script allows you to manage your links using a MySQL database. It features easy install, user submission, and an admin panel to add, edit and remove categories and links. The script is easy to customize to suit your needs.
Development Status: Alpha
License: Freeware
Operating System: UNIX
10. eSyndiCat Omega
eSyndiCat Omega is a free link directory software that can be used for a great variety of sites. Whether you build a link directory or use it like classifieds software eSyndiCat Omega can fit all your needs.
Development Status: Production/Stable
License: GNU General Public License (GPL)
Operating System: windows, linux, FreeBSD