I think that's the biggest mystery: why it's called "Harvard." Wikipedia
(http://en.wikipedia.org/wiki/Parenthetical_referencing) says:

According to an 1896 paper on bibliography by Charles Sedgwick Minot of the
Harvard Medical School, the origin of the author-date style is attributed to
a paper by Edward Laurens Mark, Hersey professor of anatomy and director of
the zoological laboratory at Harvard University, who may have copied it from
the cataloguing system used then and now by the library of Harvard's Museum
of Comparative Zoology (Chernin 1988). In 1881, Mark wrote a paper on the
embryogenesis of the garden slug, in which he included an author-date
citation in parentheses on page 194, the first known instance of such a
reference (Mark 1881, p.194). Until then, according to Eli Chernin writing
in the British Medical Journal, references had appeared in inconsistent
styles in footnotes, referred to in the text using a variety of printers'
symbols, including asterisks and daggers (Chernin 1988).

Chernin writes that a 1903 festschrift dedicated to Mark by 140 students,
including Theodore Roosevelt, confirms that the author-date system is
attributable to Mark. The festschrift pays tribute to Mark's 1881 paper,
writing that it "introduced into zoology a proper fullness and accuracy of
citation and a convenient and uniform method of referring from text to
bibliography." (Chernin 1988). According to an editorial note in the British
Medical Journal in 1945, an unconfirmed anecdote is that the term "Harvard
system" was introduced by an English visitor to Harvard University library,
who was impressed by the citation system, and dubbed it "Harvard system"
upon his return to England (Chernin 1988).

A strange feature of the 'Harvard system' is that according to Harvard's own
Widener Library, "The Harvard system is something of a misnomer (Bourneuf
n.d.)". In the UK and some of the Commonwealth of Nations, formerly the
British Commonwealth, the name 'Harvard System' is widely used, but not in
the university after which it is named. It has been said by a professor at
Harvard that "It sounds like what we call the Social Science System".