There are many books that are under-appreciated. A set that I love are R. Aryeh Kaplan's The Handbook of Jewish Thought (2 volumes). The author can be accused of being overly eclectic and of reading non-kabbalistic texts within a kabbalistic framework. Nevertheless, the organization, clarity and, most of all, the vast wealth of sources contained in the footnotes make this series irreplaceable. This is not a handbook of Jewish thought but an encyclopedia, if you are willing to look up the references in the footnotes.
UPDATE: I found that three chapters (absent the footnotes) from this series have been posted online at the Aish HaTorah website.
The Rules of Halacha
The Pre-Messianic Era
Respecting God in Speech
Sunday, July 04, 2004
Under-Appreciated Books
8:04 PM
Gil Student