Bagi,
For web directory, I will suggest you use eSyndicate or PHPLD (I am sure there are many other good script, I only have experience with the above two) If will also suggest you keep your directory section separate from the rest of your site for easy maintenace, perhaps the directory should be in a folder called /dir/ and link to important part of the directoy from the index page. This will give you more control over you homepage.
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