I have over 1800 links with thousands of freebies in my 3D Directory. I imported all the links to the database and then spent about 2 months in the evenings and weekends, cataloging, adding descriptions which list each freebie by name. It was quite a job.

The program that I use has a feature to check if the links are still active, but with 1800 links it takes quite a long time for the script to run. There is stand alone software that can also check links for a website. Whenever I find a dead link, I run a Google search to see if maybe they changed hosts.
If I don't find anything I will mark the site and link for deletion from the database. I'll generally wait for 2 or 3 days before deleting though to make sure it isn't just a router problem.

The directory also has an Add Site function, where an individual can add their site and maintain it.