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I often go with pencil & paper for the first pass through difficult code. Actually I'm likely to start with the interaction version of the diagram rather than the sequence version. It just seems easier to add more objects as needed that way. I do really like sequence diagrams and wrote a macro for my text editor to format neat text-only diagrams. Rose is a fantastic tool, but I feel committed to do really refined work when I bother to fire it up, so paper comes first.
PJ Plauger wrote about picking up a diagram by one bubble and shaking it. If you pick the right node it might shake into a tree or circle or a hub and spoke or who knows what. It's useful to try different shapes for an interaction diagram and see if one reveals a hub of dependencies or function driver.
A good question is never answered. It is not a bolt to be tightened into place but a seed to be planted and to bear more seed toward the hope of greening the landscape of the idea. John Ciardi