I keep all my files in the root directory, but it's only about 700 files so it's easy to keep them organized. To me, the main reason to have separate directories is to allow you to have files with identical filenames. But this may be because I've been programming so long and the old organize your files by using the alphabet is something I'm used to.

Some people think keeping all your files in the root helps your search engine rankings. I have no idea if this is true, but I get fine rankings.

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Sailing Texas is a site I originally made to promote my sailing classes. It has taken a life of it's own, now the most popular part is the Sailboats for Sale section, and it just keeps expanding.
http://www.sailingtexas.com/