I find this useful also, especially with new technology where I may not already have a good mental model of how it works.

I generally use Notepad++ and it's often just a set of notes about the value of important variables in certain files @ a particular line of code or at a particular time. I find that seeing that big picture at a glance can often give me immediate insight into what's happening. Something you can't always see when you're focused on a few lines of code in a method.