Usually when its a University of somewhere that somewhere is a place. So in your example 'Havard' isn't the name of the town, that would be Cambridge, Mass. Havard is the name of the man who founded it. York, Oxford, Cambridge are all towns so people do tend to say University of York etc. interchangeably. Some styles are preferred by the universities themselves, so e.g. Oxford University officially styles itself the University of Oxford.

You can see from these lists http://en.wikipedia.org/wiki/List_of_universities_in_the_United_Kingdom http://en.wikipedia.org/wiki/List_of_state_universities_in_the_United_States that they are named in both forms. It just differs from university to university.