As you can see, there's one at the top of the forums now.
Simply put, we have to have a way to pay for the things we're doing here, and the things we want to do going forward. The banners will help with that.
The plan is to only have that one banner slot under the main logo, and rotate different advertisers. Different individual forums can - and probably will - have their own sets of banners at some point.
Note: there is only one site-wide banner slot at the moment. All forums are rotating the same banners.