Suggest me some tools/strategies for brainstorming the application before jumping into the code

Up to this point I have been making small/medium size applications. I'd do all the brainstorming in my head and I'd make my design decisions in the middle of the development. But as I am moving towards larger applications I can't do this in my head anymore. I need to have my entire project plan laid out right in front of my eyes. If you are a one-man team, I am sure at some point of your career many of you have faced the similar situation. How do you handle the 'pre-production' phase of your project? What steps do you follow? What tools do you use for visualization? I need some suggestions...