Skectching paper (3' by 2') and a sharpie and pencil. I like the large surface, but find it easier to work on a horizontal surface (rather than using a whiteboard.)
I've actually modeled some flowcharts for the boss in MS Publisher. The drawing tools are good enough, and it converts to pdf. Not free, but may be on your workstation already.
I don't always do use cases, or even user stories, but will always brainstorm how a new app will be used, and by whom, before planning. That helps me better defend my specs.