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From the very start, directories have served a very useful purpose on the Internet. (One I find useful for example is Free Web Directory). News sites can also be considered directories: they index and categorize news stories! What about categorizing software? In the open source world you get Savannah, SourceForge, Freshmeat; there are still, believe it or not, shareware and freeware directories like FileBuzz, PCWin Download Center and Freeware Downloads (although you need to be careful, as they are not like their free-as-in-freedom counterparts).
About Jonathon's article Anybody Up To Writing Good Directory Software?, it's clear that the topic of software directories is very hot. Most of what you find on Google, however, are not pointing to free and open soruce software -- or worse, they mix the two. Examples of such sites are Freeware Downloads and Shareware Download, which simply don't focus on "free as in freedom", and still can be used as good free software directories.