A variety of businesses share the way that they calculate return on investment from the web portion of their business in this Internet Week article.
For example, Ryder uses a "strategy tree" to identify priorities like customer satisfaction and financial performance. Once they established a baseline with web initiatives, they were able to predict ROI with greater accuracy.
The report concluded that while there is no universal measurement that can be applied to every business, tailoring web costs to measured expenditures in your business can be successful.