This is interesting. A fairly detailed taxonomy of the existing business models for web sites. The breakdown is here. Using their taxonomy the researches than examined one Top 100 web app list for 2008 and found that:
34% use Advertising, 12% a Variable Subscription model, and 8% each for Virtual Products (typically digital downloads), Related Products (typically a large software company offering a free product to attract you to their platform) and Pay-Per-Use.
The graphic pie-chart display of those results look like this.
(I.T.A = Advertising)