Yeah, I'm having this issue too. I've applied to PhD programmes in political science, public policy, an dpublic health. My masters is public health, and regardless of which PhD I end up wiht, I'll probably be looking first to schools of public health for academic employment.
My sense of NGO/UN orgs work in my area is that the PhD is actually important - the MPH is fine if you also have a lot of relevant work experience, but for someone trying to get their foot in the door, a PhD is the go.
In terms of choosing between the three disciplines (I realise everyone else will be choosing between two) - I think poli sci opens more academic doors. Schools of public health and public policy both routinely employ people with poli sci degrees. (Having said that, I think that would only by the case in the US; if I wanted to go back to my own country and work in a school of public health, I think my PhD would probably need to be in public health.) But, I think the poli sci PhD is the least useful for consulting - working for the WHO, in my case.