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This is a short list. Not because there's only one or two organisations doing good work in Madagascar but because I would just be speculating about programmes for you to volunteer your time with—which is of little benefit. I suggest doing some serious research on any organisation and projects you're interested in volunteering with. You should be able to find plenty of project descriptions and first-hand experiences online.
What I can do is list organisations that I've heard good things about from others whose opinions I value, or had positive experiences with myself. Any omission is by no means an indication of quality or comment of any kind.