I have been trying out different banner sizes and positions on my various website sand blogs. And leaderboards -- those 720 x 90 banners placed at the top of pages -- do get more clicks than others.
This is hardly surprising, of course. They stand out more, and are the first thing the visitor sees. Also, only a small percentage of people actually read web pages all the way through, so those ads placed down at the bottom will obviously get fewer clicks, no matter how big they are.
So, if you are promoting different affiliate programs then it's a good idea to to advertise your highest paying program with a leaderboard. Do this and you could see quite an increase in your earnings.