At what point in the rankings is having a PhD from one university no different than a PhD from another (differently ranked) university? There are some websites like topuniversities and times higher education that rank universities based on several criteria.

I don't know if the ranking of a university is directly proportional to its actual reputation. 

It is obvious that top universities such as MIT, Harvard and Stanford in US or ETH, Uppsala, KTH in Europe should be considered apart from the rest, but at what point is having a PhD from one university no different than having another? Is it after 100? Between 300-400? Or is it due to another criteria than the ranking?
It's worth keeping in mind that the overall university ranking is not synonymous with how they are regarded in the field.  Even the breakdowns by discipline are not always going to reflect how the university is perceived in a specific field.  

For example, a university may not be in the top 10 in these overall rankings or even in a discipline (e.g., Computer Science), but they may be considered in the top 10 or even the top 5 for specific research fields (e.g., Database research).  

For a PhD, the ranking in the field will probably carry more weight than the general ranking of the university (depending on the field), as will the overall quality of the research.