Many websites default to the 728×90 (leaderboard) ad size when designing their site. This is a reasonably good option as it has the second highest click through rate of the various standard ad units. But it is possible to do better. Marketing Sherpa researched clickthrough rates by ad size (from largest ad unit to smallest) recently:
The chart shows that click through rate is not simply a function of the size of the ad. The largest ad unit, the wide skyscraper (160×600) has the second lowest click through rate. For the full range of IAB standard ad units, click here.