AdRotate allows you to track clicks on as many ads as you want to set up.
It also allows advertisers to have a special log in so that they may check their own statistics or even update their own ads if you want to give them that power.
It’s a pretty robust system with decent support and some cool features planned on the horizon (from what the developer told me when I asked him a question about better integration with theme development).
Note: If AdRotate is too robust for your needs, this could be implemented on your own through some Ajax calls when a user clicks on an div with a specific class. These clicks could be saved in a table or via options. But, honestly, AdRotate does it so well that I haven’t seen the need to reinvent the wheel.