This article from a list apart talks about website usability and how design choices have a serious impact on site performance.
One of the things that I love (and amazes me) about amazon is that they have a really cool framework that allows you to test any design changes to the site. Almost all design changes go through this 'weblab' process which calculates the statistical impact of a certain change on various things (purchases, add-to-carts, etc. - I don't know the actual set of metrics we track).
Design is a wierd and sometimes counterintuitive thing. I couldn't guess which was the most usable site out of the three listed in the article above. I think the discipline of constantly collecting and analyzing metrics goes a long way.