This is a process that I've been thinking through increasingly after having evaluated years of custom development work, the last two in custom Ruby on Rails development work.
One would think hourly pricing would help manage scope, but every single project has a project budget. Every project starts out with a thousand "how long will ____ take?", "How long will this other ____ take?", "It's easy to do _____, right?", etc.
Getting clients to see the value of the discovery/requirements gathering/story carding phase of the work is paramount. Too many times, people expect that to be part of the "free" pre-sales consulting that goes into the proposal writing process rather than as a key part of the software development activities.
For someone who is looking for a more narrative (parable) form of these ideas, Mike McDerment (of Freshbooks) has published a free e-book on value-based vs hourly pricing - http://www.freshbooks.com/blog/2013/06/12/breakingthetimebar....