Hi Devan,
I would do this actually as part of the "header".
This sounds strange, but actually works well. The header is on every page, and the "content" takes up the space not occupied by the header, so everything just fits together well.
You see this approach used internally when you use a vertical menu (like Accordion) - that's part of the header, but takes up the left side of the screen.
Obviously the exact mechanics will depend a bit on your app but try something like this;
<div id="ads" style="height:100%; width:150px; right-margin:15px; float:left;">
Adds go here
</div>
obviously you can make your own css class for the div. To make it float of the right set the float to right, and change the margin-right to margin-left.
the next step is probably to put it in a NetWebSouce procedure (still called from the header) where you can then flesh out the content etc.
cheers
Bruce