Depends how much of a perfectionist I'm feeling. For the initial development, a sharpie, index cards, and a whiteboard wall - or Lucidchart, because it's basically an in-browser whiteboard/drawing tool.

Once the project is ongoing and you'll need to account for changes, I've either done it manually (which takes an age) or handed it off to PM's to oversee using either MS Project, airtable with a custom-authored set of actions/etc, or PrimaVera.