WANGO is an easy-to-use website for identifying organizations that work on your issue of interest and/or work in a specific location.

Find NGOs by issue: Use the "Search" feature to specify the "Mission," e.g. infant malnutrition

Find NGOs by country/region: Use the Search form and specify the region or country.

Each country has a searchable PDF document, listing the following development-related organizations (updated as of 2011, so verify currency!). Here's the directory for Nepal, for example.

(1) international organizations
(2) government institutions
(3) private sector support organizations (including fairtrade)
(4) finance institutions
(5) training and research centres
(6) civil society organizations
(7) development consulting firms (including references to job opportunities and vacancy announcements)
(8) information providers (development newsletters/journals)
(9) grantmakers