Questionable Science Behind Academic Rankings

A recent article published in the New York Times questions the validity of academic ranking systems such as the Times Higher Education ranking list, citing the over-important role bibliometrics play in these rankings. In the case of Alexandria University, the author discusses how this university's high ranking seems to be due to the publications of Dr. Mohamed El Naschie, an Egyptian academic who published over 320 of his own articles in a scientific journal of which he is also the editor. The author goes on to discuss the problems that exist in trying to measure academic excellence, and the validity of using bibliometrics (or how often faculty members are cited in scholarly journals) as a way to measure the quality or influence of a university department.

Are there other, more nuanced ways of measuring the impact of universities, and how much weight should we ascribe to academic rankings of this kind?