i use mind mapping software like free mind [ http://freemind.sourceforge.net/wiki/index.php/Main_Page ] or concept draws mind mapper pro [http://www.conceptdraw.com/products/what-is-conceptdraw-mindmap] which is a favorite of mine. these programs allow you to lay out complex and branching story arcs and add notes concept art as it enters the pipeline. when working on a team it also helps because it lays out the big picture a little clearer than reading through a bunch of files and looking at some pics separately. i don't remember what i used to do before i used mind mapping software, with my phone now i can even create maps and open them on my computer. the last idea i mapped i did entirely on my droid.

Articy: Draft seems to have come out of Beta and now be offering free 30day trials. Not tried it yet but planning on having a go with it soon.