What do you use to organize your thoughts for a new website or project?
carbon8: Redmine. The basic pattern is usually starting with a wiki, jotting down notes, collecting links, brainstorming and dumping information I get from research or talking to people, then start opening tickets as todos start to come up, then add people to the project as needed. I do this or something like this for most tech and non-tech projects. I do have a couple moleskines, but I find using paper to be more cumbersome. Sometimes I'll use them for UI sketches. Whiteboards are great, too.