I discovered this free software for organizing your novel back when it was just plain old yWriter, and now it’s up to version 4 (for PC and Linux only¹–sorry Mac users²). It’s actually more than an organizer–you can actually write your novel in yWriter4.
Every novel in yWriter is a “project,” and for every project you can include characters, objects, locations (settings), scenes and chapters. Dragging and dropping scenes and chapters makes it easy to reorganize the story.
Some screenshots (click for larger):

When it comes to scenes, you can get incredibly anal about them. In addition to a big block where you can type (or copy and paste) the actual scene is a set of tabs: Description, Status, Goals, Time, Scene Notes, Characters, Viewpoint Details and Overview. “Status,” for instance, is where you can say whether the scene relates to the main plot or to a subplot and say whether the scene is at this point an outline, draft, first edit, second edit or done. Under “Goals,” you can say whether the scene is an action scene or a reaction scene, and define the goal, conflict and outcome for the scene. “Time” lets you say when the scene happens and what time span it covers. “Characters” lets you select the characters who appear in the scene. All of this information helps you see the structure of your story.
This software is ideal for people who are anal and love to organize, but be careful: you can easily spend all your time working on information about scenes instead of actually writing the scenes.
Finally, if you already have a draft of a novel, yWriter can import it, provided you save it as RTF. Include chapter headings (Chapter 1, Chapter 2, etc.) and scene breaks (***) in the file, and yWriter will automatically create chapters and scenes in the project as it imports.
Here’s the yWriter website: http://www.spacejock.com/yWriter4.html. Again, the software is free.
In additional to all this, there’s one more very cool thing about yWriter: you can make it run from a USB flash drive. This is perfect for people who write at work or school and at home. After you download and install yWriter on your computer, drag or copy the folder to your flash drive. Then download the “Pendrive Runtimes” application at the bottom of this page. When you run Pendrive Runtimes, it will ask where the folder is. Enter its location on your flash drive (for example “F:\yWriter4″). It will install some extra stuff on the flash drive, and then you’ll be able to run yWriter from any Windows PC.
All that said…I’m not actually using yWriter4 for Deadlock Rot (though I will be when I start the Growl Mercy revision in the spring–different books, different needs). I’ll show you what I’m using for Deadlock Rot tomorrow.
Speaking of Deadlock Rot, dialog scribbles and scene notes are beginning to accumulate in scraps of paper around my desk. I’m happy to see them. :)
Also, I’ve figured out how to sum up the book in one word. I’ve been reading James Scott Bell’s Plot and Structure this weekend (Christmas gift from my mom–isn’t she great?), and there was a point where he did the ol’ “Describe your story in a sentence or two” thing, which…I’m so not prepared to do with this story yet. I think I need to get through much, if not most–if not all!–of it before I can compress it back down to a few sentences. But I have a word now (which means I’m probably onto a theme, too): obsession.
Last night as I was falling asleep, I realized that that was the one thing my three disparate main characters had in common. (Okay, the one of two things: they’re also all male. But anyway) Derrel is obsessed with something he believes is rightfully his that has been withheld from him all his life. Jeff is obsessed with collecting refuse. Or, actually, he’s obsessed with staying right where he is; collecting refuse is a mechanism he uses to keep his life from moving forward. And over the course of the story, David becomes obsessed with his Tragic Hero. I think he was looking for a Tragic Hero all along.
David’s my narrator. I think he’s going to do an all right job.
¹Linux users should read the note on the Download page on how to get it working on their system.
²There is a similar program for Mac users: Jer’s Novel Writer.