When you are starting research and still scoping out a subject, looking at a directory can be very helpful, particularly when you're not sure how to narrow your search. The directory can help you understand how topics within a specific area are related. Students often need this approach so they won't get mired in the details too quicly. A directory can give you 5 good sites, not 5 million pages - and which do you really need?

Yahoo! originally started out as a directory, and only later added the search engine. They still maintain their own, while Google leverages the knowledge and some of the technology behind what's called the Open Directory - a collaborative project, sort of a precursor to wikipedia, where anyone claiming special knowledge could pick the sites for a directory topic.

Another excellent directory that is well maintained is the Librarians Internet Index (LII), a publicly-funded website (no ads or sponsored placements for links!) and weekly newsletter.

Grokker is not really a directory, but it takes the results of Yahoo!'s search engine and turns it into an on-the-fly directory, a little like what Clusty does.

Some of the best "homework help" sites break things down into understandable categories that map to school subjects. The Multnomah County Library has a great one, with helpful annotations to boot.