This page is a continual process. Return often. :-)
Newell, W. H. and the Association for Integrative Studies. Interdisciplinarity: Essays from the literature. College Board (December 1998). 563 pages.
Repko, A. F. Interdisciplinary Research: Process and Theory. Sage Publications, Inc (May 29, 2008). 416 pages.
Strober, Myra. Interdisciplinary Conversations: Challenging Habits of Thought. Stanford University Press (2010), Hardcover, 232 page
XMind Mindmapping Software
CMap Tools - concept mapping (I've yet to try this, but it looks amazing)