I live and work in Geneva, the NGO capital of the world. Just in order to pay their overheads, organisations here need solid core funding. Switzerland must also have one of the highest costs of employing staff in the world. This usually means that when an NGO wants a funky web site, they can often afford to pay a commercial developer up to $1000 per person-day to build it.
(My mission in Geneva, by the way, is to lower that cost.)
There is also sufficient networking spirit in this Geneva that the technical people, web managers, or knowledge managers in these organisations have access to anecdotal information about such projects, and can approach them realistically.
Smaller organisations though, with less money and connectedness often do not know how to approach web development. One organisation I know spent 18 months iterating though pixel perfect ideas for their graphic user interface, hoping both to save paying a designer and to express and think through completely what the site was to do. Another organisation had committed a full developing world salary to web development, yet the site was cluttered and clunky and half the salary went to updating content.
Organisations do not know how much web sites cost, what it means to have a cheap site, how to engage with serious web developers, or how to manage expectations for a software project. It is worth calling in an independent advisor to talk over your project, and help guide you through it. That's why I'm offering one free hour to any non-profit (in Geneva) to talk them through the process of developing a new site.