There are a number of ways of doing such, iSkywalker... I have an ad module installed on my WP site, (AdRotate), that I feed from a backend system, which powers all of my sites from one central point... The backend system is Open X - http://www.openx.org, which was once known as phpAdsNew till not long ago. Open X, is open source, so you can pick a copy up for free and host it yourself, or use their hosted version... Either route you go, I think you will find it to be quite powerful...
Personally, I would like to see an addon like AdRotate that actually takes into account what level a user is, for example, showing more ads to a subscriber, then to a contributor, or if you had the ability to define more roles, such as membership levels, to reflect those who had directly contributed to your site's development and survival by showing less / no ads, etc...