Software

MInd Mapping

XMind (free) – example

FreeMind (free)

Think Buzan/iMindMap (paid) – example

Diagramming/Flowcharting

yEd (free) – examples

Dia (free)

Diagram Designer (free, Windows only)

OmniGraffle (paid, Mac only)

Visio (paid, Windows only)

free/open source office programs such as OpenOffice / LibreOffice also have diagramming tools built into them

Tutorials

System Diagramming tutorial