A well developed site, (good PR, traffic, members/revenue if appropriate), should be worth as much as its dot com equivalent. Only if the domain name is exceptional should it really affect the price.

Let's take skype.com as an example. Without the product/site/members/traffic/revenue behind it then the domain name would be worthless. In the same vein, if the company had been built around skype.ws I'm sure it would have sold for just as much.