It's funny how you can think you pretty much know all the top-tier Open Source applications that are available ... and then you find a program like Protégé.

An open-source (MPL) ontology builder and knowledge base engine, the program is clean, responsive and easy to use. It's Java-based, which all too often is a synonym for "slow and clunky" or "really ugly" but in this case, just download the installer (even a standalone JAR installer worked first time on Windows) and it's up and running in 2 minutes.

The obvious comparison in terms of quality (again, thinking of Java programs here) is FreeMind, a thoroughly capable mind-mapping software program.

Lots more to explore, but generally highly, highly impressed. Kudos to Stanford for this one!

UPDATE: Oh - I forgot. Props to Steven Jenkins for his excellent PPT presentation that outlines this and other useful Systems Engineering Tools.