I write this blog post based on exactly one day of using Scapple. But I'm already convinced it's a fantastic tool. To explain why, let me first describe the tools I've used heretofore. I currently (and probably forevermore) use a Mac, but I've tried to note Windows equivalents where I have personal experience with a good one.
Treed! for iPad: This is an excellent program for project planning, i.e., goal-oriented planning. Its premise is that you have a final goal, and you add in all the points that lead up to it. Some of them are what we in the business world (well, formerly in the business world) call "dependencies." E.g., you can't put the cake into the oven until you first mix the batter, and you also have to preheat the oven. These are two separate tasks that have to be completed before putting the cake in the oven, but neither one of them has to be done before the other, and each of these in turn may depend on further tasks, like walking to the oven before setting the oven temperature (if you really want to get that detailed). With a little thought, you can see how this method could be transferred to writing a book: John Doe has to die before Bob shows up to investigate the crime scene, but Bob doesn't necessarily have to kiss Alice before Alice buys a cruller, and so forth. Treed! makes building the tree easy, and makes alterations to the tree (which you will inevitably need to do) equally easy.
Tree (not to be confused with Treed!) for Mac: Lets you organize text, whether phrases or paragraphs or chapters, into a collapsible tree (the way Windows Explorer lets you view folders with the little plus/minus signs). Great for outlining and all sorts of other note-taking. For Windows, there's a similar program called Treepad I used extensively before switching to Mac.
MindNode for Mac: A "mind-mapping" program. Like Treed!, everything ends up pointing toward a single root node. Come to think of it, topologically the two programs are the same, though for a goal-oriented project the more linear Treed! layout is more intuitive (but requires more scrolling). MindNode is an easy-to-use and visually appealing program, but for brainstorming, I need something that imposes less structure, while still permitting me to create structure when appropriate.
Index Cards for iPad: An app that lets you create a grid of index cards, rearrange them, and form stacks of cards as needed. Aside from Scapple's ability to draw links and arrows between notes, this is probably the closest thing to Scapple on the list. Unless speed isn't a factor, in which case the closest is...
TouchDraw for Mac: A diagramming program. Easy to use, but doesn't support the same level of sheer idiot speed as Scapple does. The trade-off is speed of use versus speed of making things look professional. If you need to show your work to your boss, use TouchDraw (or spend some extra time in Scapple making it look fancy). Similarly worthy programs for other platforms include Grafio for iPad, and SmartDraw for Windows.
So, what you get with Scapple is a perfect (or darn near perfect) balance of speed and versatility. At present it's only $15 on the Mac App Store. And there's a ton of reviews out there on the Interwebs, so if you think it could be at all useful to you, check it out.