for keeping track of order of plot events, Twine is a pretty good way to go. it's normally used for creating branching text adventures, and because of that the format of the program is like putting sticky notes on a wall. which is what i used to do, until the sticky notes started falling off. :B
and Evernote's pretty fancy. you can have notes in different notebooks and add tags to them. they can be used to keep scripts and character notes.
if you use Windows, then yWriter is amazing for organizing chapters, scenes, props, and characters. but i had a friend whose yWriter files got corrupted, so... be sure you keep a backup for your story in case that happens.
I also have a cheap pad of paper where thumbnails and scripts and character notes are jotted down on the same page and over each other -- the mad clutter somehow feeds the brainstorm -- but i don't recommend relying on that haha.