Archy, the common way of earning from directories is this :

As the webmaster, you can give offers of no reciprocal link-required features to be listed in his directory.

For example, almost all Free directories require members to place a reciprocal link that leads back to the free directory. You can offer a paid membership to the members that will not require them to have a reciprocal link and maintain their site's professional and clean look.

Example :

w/ reciprocal link - Free
w/out reciprocal link - $9.99 per month
premium + w/out reciprocal link - $19.99 per month

Very easy money as long as your directory is famous.