Ask HN: tools/methodologies to collect and flesh out idea's

I've got a collection of idea's that I'm constantly adding to when I think of a project that I want to work on some day. Problem is that this collection is spread out over several media. I have a moleskin that I take notes in, use evernote and/or pinboard to save websites/tools I want to use on one of these projects, etc ...<p>How do established founders actually collect their idea's on new projects and flesh them out? What tools and methodologies do they use?