I usually keep a notepad and pen with me at all times. So, if I'm out thinking about a story and a scene or a bit of dialogue comes to mind, I write it down for recall later. I also keep a list of things that need to be added or changed in the story in other places. Say, I'm working on chapter five -- writing or rewriting -- and I realize that what's happening there requires a change in chapter one, I write down the change in a list in my notebook to make later.
Lately, though, I've been using Evernote as sort of a digital journal for my writing. There are iPad and iPhone versions, too. I'm kind of torn, because I love having the handwritten notes to look at later. So, my question, is do you keep a writing journal to help organize thoughts and ideas and -- what do you use? A Word file, a paper notebook or something like Evernote? Are there any apps out there specifically for writers?