Graphviz
A mature open graph-visualization toolkit that lays out nodes and edges as hierarchies, networks, and relationship diagrams through DOT and related languages.
Why use it
Technical and systems designers can keep skill trees, dependencies, quest networks, and state relationships reviewable, generated, and version controlled.
Where it fits
Use prototypes and playtests to find core experience problems while they are still cheap to fix.
What to check
Automatic layout does not guarantee clear communication and dense graphs still need decomposition; DOT and renderer options take learning, and interactive prototypes need another tool.