I would probably say that the most universally popular leader of a country still living (but not still leading a country) is Nelson Mandela--someone who managed the transition to post-Apartheid South Africa by holding a country together with his charisma and the force of moral leadership. Of course, S. Africa has problems, but without someone like Nelson Mandela, the transition could have been horrible.
Another way to look at it is this way: there are many popular leaders out there, but many of them are hated as well (in the US, for instance, both Bush and Obama are enormously popular with _and_ hated by different groups of people). I haven't done a poll, but I have trouble believing that many people out there hate Nelson Mandela.
Let me give you an example: I know a white South African who my inlaws were friends with. During the 1980s, before the fall of Apartheid, he _defended_ Apartheid, saying it was better for blacks and whites; he and an Ghanian friend of my inlaws almost came to blows.
Several years ago, I met this same white South African man. He ended up working for Mandela in the 1990s. He spoke of Mandela in such loving and respectful terms ("He was born to a family of great chiefs, you know," he told me) that it was hard to believe that he was ever in favor of Apartheid.
To me, someone who has that kind of an effect on people, to change their minds, to unite a divided nation--THAT is a leader.