Linux can do many things, I'm not particularly well-versed in the uses of NGOs, but email and communication shouldn't be an issue on linux, managing donations you could probably find some way to work it out.. you may want to look at pages like the FSF's free software directory to see what kind of relevant programs are available (
http://directory.fsf.org/wiki/Main_Page)
With that as a starting point you can probably figure out what it's capable of doing, since it's all free software on that site it's all free to be modified and used for whatever purpose.
As I said I'm not well versed in NGOs or their particular needs, so I can't recommend anything really beyond looking at the available software to see how free software can address the needs of the organizations in question.