CMAP - Knowledge Modeling Kit developed by the Institute for Human and Machine Cognition (IHMC).  The IHMC CMAP Tools software empowers users to construct, navigate, share, and criticize knowledge models represented as Concept Maps. This is a fabulous tool that I use on a daily basis.  I use it for creating visual maps from elicited information and also as hyper linked "front ends".

Mind Map - Mind mapping software from Mind Jet "helps align people to work smarter, think creatively and save time by visually capturing, organizing and communicating ideas and information effectively."  Another great tool that should definately be part of your knowledge capture arsenal. 

One Note from Microsoft is a great notes organizer that offers the ability to record from your labtop (both audio plus video via webcam) and integrate these into your notes. Good search ability that's useful during conversation with the SME - you can go back to where similar topic was discussed both in your notes and on the audio and link new information on the spot.

Interactive Point of View (IPOV) - Video capture and production services focused on knowledge capture