Not all, but most.

• Everything (except Microsoft Windows) we use in class is currently easy to download from the web.
• Protege, SWOOP, Jena, and other key tools are all open source java with agreeable (e.g. Apache-style) licenses.
• For text editing, we choose to setup both JEdit (open source Java) and gvim (charityware C implementation of classic "vi") on client workstations.
• The limited scripting we use is based on BeanShell (open source Java, well integrated with Protege and JEdit).
• The rules engines we advocate using for production systems (Mandarax, etc.) are also open source java. However, for convenience we currently teach some Protege examples using rule engines that require commercial licensing for any use besides academic research.  The use of these tools is always made clear to our students, and the alternatives for use in academic and commercial environments are presented. A key strength of Protege is the stability of its plugin framework, so students will always have a choice of tools to bring back to their working environments.
  
• We use various C programs mainly for web browsing, text and graphics editing/display. Most of these are open source but, for example, it is still convenient to use Adobe's SVGViewer and the Macromedia Flashplayer sometimes. These tools are freely downloadable, but not open source.