Concept Maps are a useful way to graphically document the relationships between the elements of a system. Not only do they assist in the system design process, but they can be used to communicate design ideas to stakeholders such as users and management. Unified Modeling Language (UML) is a more structured form of concept maps focused on Object Oriented Programming (OOP.)
We've found that combining tools and including useful graphic elements such as screen shots creates a very user friendly design tool.