How integral is this directory to your site? The latest theme from Elegant Themes
(my affiliate link), called "eList," turns your site into a traditional directory listing. It could be a jobs board, a dating service...anything Craig's List-like, basically.
If a directory is supposed to just be a part of your site, as opposed to the heart of it, you can still implement a whole theme (as opposed to just a plugin) by hosting it as a subdomain.