Change your banners often. After a few hundred thousand impressions a banner becomes stale and it's click-through rate will drop. Track your banners constantly. You need to know what works and what doesn't, and that this can change daily. Keep those banners that work well so as to rotate them back at a later date.
Banners take up valuable web real estate.
Your search pages are prime also. You are not limited to banners. Use your favorite search engine to find button exchanges and link exchanges as well. Check out these sites for free exchanges. These tools can be used for other applications as well.