Hi thebigaym,
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/) but you could just as easily use any sort of ad service that provides ad display HTML. Basically, you will need to configure the ad software and create some ads, which should also provide you with an HTML/Javascript code snippet to insert into your website; then you copy that code and either add it to a template file (say your templates/common/footer.tpl to add an ad to the footer) or create your own block (using the Custom Block plugin, or manually) and add the code there.
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!
Cheers,
James