What I like right off the bat is the category structure. It appears that you started with only top level categories, meaning we don't have a lot of empty categories floating around, and that makes for better distribution of content. What I also saw is some categories may need to be split up a little with sub categories now, as there are many pages. It shouldn't be all that time consuming to create a couple of subcategories, then use the multiple select and move in the phpLD admin interface.
I like the Webmaster Tools over on the left column. You figure a lot of people who submit to directories also use webmaster tools, so hopefully you are getting some click throughs to these sections.
Some categories like Pharmaceuticals may attract some spammy links, so I would make sure you have a good review process. Also, you might want to consider adding some of your own links to these categories and sort by something like pagerank (but don't show it). This will help insure there is quality one click from the homepage, and more questionable links deeper.
So good luck with your directory, and hopefully we'll take a look at it again in a few months!
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