Your Q is very valid and relevant: we in India have an obsession with figures and the number of NGOs is mindboggling. While there are many doing good work, a large number of these NGOs are either corrupt or fronts for nefarious activities. Please Google and do your own search, e.g., this interesting site:http://www.interventions.org/fraising.html
Personally, I follow the practice of donating either through funds launched by main newspapers/magazines or personally to deserving individuals.