Apartheid is, like fascism, a term that has been abused by people using it to describe innumerable situations more or less distant from its prototypes (South Africa in the first case, Italy in the second). Even so, when used carefully by people who are able to be quite specific about what they're talking about, they're still useful terms. Fascism, for instances, works effectively as a label for Italy in the 1920s, Japan in the 1930s, Nazi Germany, Spain in the 1950s and Portugal in the 1960s despite the vast differences between these five countries. I don't see why apartheid, properly used, can't be a term of similar flexibility.
One somewhat surprising discovery that seems to have come out of the discussion is the reality's of apartheid's similarity to normal practices of the modern state, indeed to normal human behaviours. As a single example, two posts linking to my GNXP crossposting related my definition of apartheid to restrictions on international migration and hostility towards evangelical Christians. People like boundaries, it seems.
That's why I think that the question of motives is the critical factor that inspires people to support policies of apartheid. Processes and policies which exist elsewhere in the world seem to be accentuated in certain cases. In the prototypical apartheid society of South Africa, the culture of Afrikaners seems to be marked by a fear of obliteration; recent articles of Johann Wingard at Global Politician come most immediately to mind as textual confirmation. The Afrikaner national mythology is one of a people beset at all sides suffering enormously for its troubles, most notably because of the concentration camps of the Boer War, with appalling death rates creating tens of thousands of martyrs. These dead, along with the instability facing Afrikaners in the generation after the conquest of the Boer republics and the formation of the Union of South Africa, seem to have inspired a certain sort of bloody-mindedness. Is this bloody-mindedness the critical factor in pushing a society towards apartheid?