One of the issues that always arises when your site starts to take off is managing ad inventory. With Wordpress, managing ad placement is fairly simple. You just create a widget, drop in your code, place the widget, and you're done. But what if you need to change it often? Or, what if you have sold your own clients and want to traffic your own ads?
Well, you are in need of an ad management system. There are some basic ones (in the form of plugins) available through Wordpress, but they are not terribly sophisticated.
Until Google opens its new ad management system up to the public, I recommend using OpenX (formerly known as phpadsnew) to serve your ads. It's a free system you can download and install on your own server. I also recommend putting it on it's own box if you plan on serving a lot of ads, or you site gets a lot of traffic. The system itself is pretty resource intensive.
You can then set impression levels, goals, and weights for all your campaigns. This makes it especially valuable when evaluating new ads or campaigns.
Let's say you want to test some new ads. Upload them all into OpenX and give them equal rotation. Wait a few ways, and check back into OpenX to see how many clicks each ad received. Then up the weighting or impression level of the one that converts the most, and lower the under performing ones. Test a few days more, then evaluate the results.
You can adjust your ad formula/mix all from within OpenX without having to constantly change or swap out code on your site.
This platform becomes even more useful if you run more than one site or have affiliate sites. You can provide your affiliates with code to drop on their site, and your ads will display. Then you can control what ads feed in there without your affiliate needing to change the code.
So, if you're at that stage where ad management is becoming a chore, think about making the jump to OpenX, or wait for Google's Admanager to come out of beta.