Apologies for the delay in getting back to you. We actually provide ad display capabilities to some of our journals. We use the Open Source Openx application (http://www.openx.com/
There is also the OpenAds plugin, which you can use in conjunction with an installed OpenX application server -- you can find the plugin in System Plugins -> Generic Plugins. I haven't used that plugin before, so I'm not sure what it's function or capabilities are, but it does point to a README file that should be useful.
If you have any further questions about this, just let us know!