Google loves and
needs directories. Directories help Google decide to what category a website belongs, what are its real keywords, etc. Cutts said explicitly that it is OK for directories to charge a review fee.
I think that "featured links" may, in some cases, be targeted; although in most cases they are OK, since they are relevant.
What is certainly targeted are sitewide irrelevant links. These are not only useless to Google; they actually tend induce Google in error.
What is also certainly targeted is duplicate content. Your directory is likely made of listings which have been written by submitters - webmasters who copy and paste the same title and description in thousands of other directories. You should try to implement duplicate content filters, or manually rewrite all descriptions to avoid such a duplicate content penalty.
All that from a directory user (not owner)
