My working bibliography of research on anthropology of universities (a woefully underdeveloped field) isn't quite ready yet. But for the time being, the obvious places to start are as follows:

• Pierre Bourdieu's Homo Academicus (1988, Stanford UP) and (co-written with Jean-Claude Passeron) The Inheritors are the modern classics in French sociology of universities.
• Richard Wisniewski, in "The Averted Gaze" (2000, Anthropology & Education Quarterly 31(1)), chronicles much of the existing anthropological literature on American universities in order to lament it.
• Cardinal John Henry Newman, The Idea of a University (1852; reprint 1996 Yale UP), is the classic philosophical reflection on the liberal arts university. For founding statements on the German research university, see Kant's Conflict of the Faculties and Wilhelm von Humboldt's "On the Spirit and Organisational Framework of Intellectual Institutions in Berlin" (1809-10; reprinted in Minerva 8).
• The best-known ethnography of an American college is Michael Moffatt's Coming of Age in New Jersey (1989, Rutgers UP); a recent, controversial study along the same lines was published pseudonymously by "Rebekah Nathan," actually Cathy Small, entitled My Freshman Year (2005, Cornell UP).
• For a political-economic study of changes in higher education, see Sheila Slaughter and Larry Leslie, Academic Capitalism: Politics, Policies, and the Entrepreneurial University (1997, Johns Hopkins UP).
• Some more critical recent literature (part of a vast critical discourse on universities) includes Bill Readings' The University in Ruins, Wesley Shumar's College for Sale: A Critique of the Commodification of Higher Education, and Davydd Greenwood's "The Reconstruction of Universities: Seeking a Different Integration into Knowledge Development Processes" (Concepts and Transformation 2(2)).
• Linguistic anthropologists have recently made some interesting contributions. See especially Donald Brenneis's "New lexicon, old language: negotiating the 'global' at the National Science Foundation" (1999, in George Marcus, ed., Critical Anthropology Now); Bonnie Urciuoli, "Excellence, leadership, skills, diversity: marketing liberal arts education" (2003, Language & Communication 23); Dominic Boyer, "Foucault in the Bush: The Social Life of Post-Structuralist Theory in East Berlin's Prenzlauer Berg" (2001, Ethnos 66:2).