I've posted about graphviz in an earlier post. Basically, I find it immensely useful to sketch out gameplay ideas in terms of dependencies.

Flower Power Example

Suppose you have an idea for your game, a "flower boss". To defeat this boss, you imagine the player attacking it with a fertilizer bomb. In Graphviz:

flower_boss [shape=octagon]; // we want bosses as octagons
flower_boss -> fertilizer_bomb; // beating the flower boss depends on the f-bomb

fertilizer_bomb [shape=box]; // items will be squares