One of largest costs in any web design project, and often the most overlooked is what I've been calling the "cost of certainty".
Some companies work out user-testing and place a lot weight on investigating the effectiveness of a design and other don't. Wherever it should lie depends a lot on the project, but most design companies seem to forget to work out with the client how much time and resources are put into that sort of work.
That's scary for clients because when they get back five different proposals from five different companies that have drastically different costs they can feel skeptical that any of the companies actually know what's going on.
It's easy to group with "quality" but I don't think it's the same. Sometimes it's worth proving or demonstrating the effectiveness of something.
If design companies discussed this more deeply with clients, I bet budgets would be a lot more clear. The differences between costs would make a lot more sense. Plus it would make the decision less about a cost and more about an investment.