If you really want a tool that can do it all... this is it!
Scrivener is one of the best apps for writers because it was built to give them the tools they need to draft ideas, compose words, edit, organize, and output their work. It's inexpensive, and the fact that you can install it on multiple machines adds value because you can work on your writing from any computer or iOS device with the app. The app is packed with features that could take ages to explore. That said, the app is structured in a way that lets you jump right in if you'd prefer to stick with the basics and just get on with writing.
Creating notes is as easy as double-clicking anywhere on the page; making connections between ideas is as simple as dragging and dropping one note onto another. And unlike real paper, in Scapple you can move notes around and never run out of space.