Well, you can use something like AdSense or you can set up several affiliate programs targeting approriate directory, for example, if you have section on health care you could show offer for weight loss or skin care products, etc. So it would make sense to visitor and probablt good return for you.
adsense, also eBay is alright to have there too. $12 per sign up and a percentage of the final price earned by eBay on auctions linked from your site
You can try our affiliate program, it is closely targetted to the people that do directory submissions, and pays up to $52 per sale. http://www.articletrader.com/affiliates/ You can even link to our directory tracker tool, something directory submitters will find really usefull. (plus we pay *lifetime* commissions, great opportunaty to snowball your earnings)
If you want to join my affiliate program pm me I have all promotion techniques covered for all my affiliates, from ebooks to emails