Web server structure?

Hi everyone. This isn't exactly HTML related, but I figured you guys know a lot about *hosting* all that HTML as well! :)

Anyway, I was wondering what the common practice is for structuring your directories on your hosting server. Is it still normal to put CGI scripts in their own directory? Is it better to put everything in a single directory?

For some things, like images, it seems maybe beneficial to keep them separate, just to be orderly. But, assuming there are no server/provider limitations on where you can put things, is it better to put static and dynamic web pages in the same directory? Does anyone still use a /cgi-bin directory, for example?

Thanks!
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