I'm currently writing a white paper discussing the cost-benefits for NPO's to switch to Ubuntu Linux as their primary desktop platform. I would be interested in talking to individuals from NPO's that either have switched or are considering the switch to get some ideas of the challenges and concerns your groups have (or had). Please feel free to contact me via email if you would be interested in providing your feedback.
To the original poster of this thread: Many of the people who have replied to you have given very weighted advice in favor of proprietary commercial software. I am of the opinion that NPO's should not be victims to the money-making agendas of corporations. Even donated software comes at a very high price for most NPO's. Depending on what your users are doing, running a free alternative, like Ubuntu Linux, is not only a more affordable and truly viable option, but the philosophy behind the free software is compatible with the NPO business model.
Organizations like Cannonical (the company behind Ubuntu Linux) offer the option of desktop support contracts at a variety of levels to meet the needs of companies that might not have a dedicated IT person. Similar contracts offered by commercial software vendors are not specially priced for NPO's, or if they are, they just aren't affordable for most NPO's. Additionally commercial software requires purchasing new licenses and hardware in order to upgrade, and if the company grows, the costs of licensing and upgrading expands.
Linux, on the other hand, is scalable (no license cost for either server products or desktop) and the goal of Linux distributions is not to make money but to provide a service (similar to the NPO business model). It is reasonable to expect users that require advanced features of specific applications (like graphics software or certain productivity tools) to continue with a proprietary platform. However, it is worth considering if an entire organization needs to support the proprietary platform just because only a small number of users require it. A more cost-effective solution is to move the majority of the organization to Linux. Supporting one or two installations of proprietary commercial software is much cheaper than supporting 100, and the overall company workflow isn't degraded.
Technical consultants who advocate commercial solutions from a single corporation typically have invested in that corporate vendors solution and are primarily focused on making money, either for themselves or for that corporate vendor. These consultants perpetuate the misconception that a certain company represents the "Industry Standard" when that is far from the truth. Market saturation does not equal a standard, it just means they have invested in a complex marketing strategy to make more money for the company with little thought for what is actually best for the industry.