Good documentation makes good software, not the other way round.

Mind-mapping

• FreeMind

Building documentation

• Simplest thing : GitHub wiki & pages
• As a service (installable version exists too) : Confluence
• API doc as a service : ReadMe.io
• Tool : Sphinx

Make it visual

• Graphviz
• Visio (well, I would avoid this one, but it’s still widely used)
• ArgoUML
• Dia