Tools for knowledge mapping vary from MS Visio or Inspiration for flow charts and concept maps to specialized software such as InFlow and NetMap. I guess the important question to ask is, what are you mapping for?
a) To compile an inventory of knowledge artifacts and find tacit knowledge wellsprings?
b) To chart the speed source, destination and constraints on knowledge flow?
c) To track compliance with established knowledge practices? (capture deviations, exceptions and critical parameters)
d) To search for knowledge related opportunities? (technology, cultural or practice related)
e) To discover communities of practice and emergent knowledge roles? (gatekeepers, stewards, translators, ontologists)
f) To trace, value and locate intellectual capital and audit intellectual property?
g) To document existing knowledge practices and plan interventions?
h) To guess at where you can reap the greatest ROI?
i) To discover knowledge needs and decide on an architecture or technology?
Each of these requires different techniques and tools. When you plan your knowledge mapping exercise think deeply how you will separate and account for the knowledge resident in people vs. that in static objects vs. that embedded in structures and processes. Consider what aspects of the knowledge cycle you wish to pay particular attention to e.g. creation, sharing, storage, transformation, exchanges, distribution.
You can map knowledge using structured questionnaires, open ended questions, one to one interviews, ethnographic observations of work tasks, video analysis, summary of network transactions, collecting sales stories or lessons learned. You can use pen and paper, palmtop, electronic notebook, word processor, database, text or data mining tools.