I can't recommend FreeMind highly enough. It easily gives you a ten IQ point advantage, in terms of being able to create insights you wouldn't have been able to see otherwise. Anyone not using it might as well be eating paint chips.
I have tried FreeMind on several occasions and my biggest frustration point with it is that it is a tree instead of a graph. Is there an easy way to get around this? Many (most?) of my ideas interconnect and it would be nice to be able to organize them non-hierarchically.
Most ideas do interconnect, so at first it would seem that the best way to model a system would be using a concept map. But forcing yourself to think in trees usually leads to much deeper understanding. This is because you end up listing examples of something, or arguments for and against things. And once you retrain your brain to see see the connections between the arguments and examples, you see that this is infinitely more valuable than just being able to see the connections between concepts.