Ask HN: What do you use to organize your thoughts for a new website or project?

I'm in the early stages of planning a website, and for me this means jotting down lots of thoughts and ideas as I work to develop the feature-set, user roles, descriptions of expected model/view/controller structures, and other pieces of information that go along with every project. Previously I've used a basic text editor to organize this information, but given the scale of my new project I'm finding it lacking ... particularly since I have a need to share and collaborate with a business partner on some of these concepts.

I've tried a variety of tools ... both online, and offline ... but my desire to keep the project concept private until it's ready to launch, and my paranoia about how private the online "note-taking/project manageemnt" tools really are have left me going back to a text file for organizing all of my thoughts.

What do others use to organize this type of information? Is there something better out there?