I found it so difficult to keep up with all my ideas until I found One Note.
The number of completely separate files I had on my computer, with a random 'ides' file not at all making any sense. It bothered me. I would also find myself flicking between ideas but not wanting to save-close-open new file. In One Note everything is open and accessible at once.
I'm going out on a limb here ... nervously posting a screenshot. I've blurred out some titles ... need to keep some secrets ... *grin*
On the left you can see all my general groups and story ideas/names. On the right you can see all the pages/chapters within the story I'm currently looking at. In the centre is that story. You can see that this is my 'timeline' workings and major scene ideas.
Exactly same notebook viewed online - which you can setup through SkyDrive without buying OneNote for the computer.
And to those of you wondering about the story showing ... it's deeply, deeply Smallville and I doubt I'll be posting it here. It's completely full of spoilers and I don't want to spoil Season 9 and 10 for you Virginia.