I have used a ton of different mind-mapping, flow-charting and graphing applications on Windows, Linux and Mac OS X and they all have specific positives and negatives. The ones that are the most complex also tend to be the slowest to rapidly diagram with but have the most features to really enable complex rendering.
Xmind (http://www.xmind.net) is a great cross-platform solution for basic mapping of structures and data. It is a topic/sub-topic mapper so it is really useful for elaboration on database structures and single concept diagrams. Xmind is a very rapid tool with keyboard shortcuts to quickly add topics and sub-topics which allows you to get a structure up and going fast so then you can tweak after you get the data out there.