Since search algorithms are just programs without intelligence they must rely upon the intelligence of humans to structure their search results.
Some search engines such as Google make it extremely rewarding for a webmaster to list their site in many different directories. Building links from many different websites from different IP ranges meshes your site into the fabric of the web.
Listing your site in a few dozen directories also strengthens your websites relevancy and position. If some of your more powerful links are not indexed for one reason or another your site can still be considered relevant by search engines on many topics based on the fact that you have inbound links from many different IP ranges.