I agree with Mike Peel on 'maybe' - I think donations from the WMF to non-profit organizations could be great and very useful, but that the WMF should
1) ensure that the donations have a substantial impact (i.e. not $500 to ICRC, where WMF funds would get lost in a sea of other contributors), 2) that donors have a strong track record of management such that the WMF does not find it necessary to oversee how the funds are used (i.e. a donation and not a grant), 3) and that the mission of the organization is linked to the overall mission of the WMF (avoid general "good thing" advocacy such as is sometimes suggested on this list).
I'd also personally support in-kind donations (i.e. dedicate an FTE or portion of an FTE to integration work that benefits a non-profit, or implements a feature that is requested for a specific platform, etc.). Training or consultation provided by a paid employee to a non-profit at no charge would also fall into this category. I don't know that it would be beneficial to have the vetting process be community driven, and I'd like to see the implications for affiliates considered (i.e. does the WMF/FDC have a position on whether affiliates should be redirecting WMF funding to third party non-profits?).