Note : I have to state that beside the university rank systems’ website, Wikipedia is used as the main source of information, so some may doubt the validity of the information. I use it since I don’t know any scientific sources. I don’t have any experiences with universities stated below, nor even have contact with people affiliated with these universities. I haven’t found forums and blogs that discuss about "underrated" universities in international scope yet. Many are only about universities in specific countries (I found USA, UK, and Phillipines). Many others analyze university rankings and are not specifically about these "underrated" universities.
When I applied for graduate study, I heavily relied on universities’ ranking systems, especially Shanghai Jiao Tong University’s and Higher Education Evaluation & Accreditation Council of Taiwan’s (no, I don’t count the THES-QS’) (shame on me!). I often underestimated universities outside that rank. However lately I found that choosing university can not be done only by taking into account such rank systems. There are many "underrated" universities, that do not present in the list or ranked low (and this description applies each time I write the word "underrated" in this post). Below are in my opinion some of those :
1. Tilburg University. My friend who is studying in Netherland said that the Economy-related programmes are highly selective and entering those programmes will be as hard as Oxbridge.
2. Some former parts of University of Paris. How can parts of such a legendary university disappear from that list? Is it because of they are not focusing in natural science (I am referring to the kinds of Paris I)? Or it has been represented by other universities such as Paris VI, 11, etc?
3. Moscow Institute of Physics and Technology. Referred as "MIT of Russia", it is one of highly-appreciated Russian university in the former USSR area, but less known abroad. I, myself, have just found out this university only from School of Computer Engineering at Nanyang Technological University, Singapore (in which I will study shortly 
) since they have an agreement in a double degree program. Probably due to their unusual educational and research system (see Wikipedia), they fail in the university rankings.
4. Gakushuin University. Being relatively "unknown" in international community, this university remains an elite university in Japan (I get this information only from a short article in Wikipedia, so if I am being eirrelevant, please correct me. However, why would Japan’s members of royal family apply to this university if it is only of middle or even low quality and reputation?)
5. Warwick University. As a top-tier university in UK, it ranked quite low in ranking systems. I think its rank should be higher…
6. French "Grande école"s. Probably since ecoles are only focused on certain (sub)field of study and theirs staffs are also affiliated with other institutions such as nearby universities, the number of published papers and staffs are not counted as done and worked within these ecoles. People who are not familiar with French education system (such as me) may not recognize them as good places to study (I read about this somewhere several months ago, but I can’t find this article anymore).
Any criticisms and suggestions?
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