This is a hotly contested subject among those who use software to write. Even something as simple as Word, it's contested. There are plenty of software programs out there. I have some on my desktop. I've tried a few, but my heart belongs to Scrivener.
I'm a pranster as plotting makes my head ache. And though Scrivener is great for those who like to plan out their novel, the cork board is awesome for someone who writes as I do. It's a screen made up of a cork board with the ability to develop index cards. Each card can be given a heading and then an area below where you can write a short snippet on what the scene pertains to.
The beauty of this is, when a scene strikes me, screams to be written, I can label my index card on my cork board, give some information on what the scene deals with, and then with a click, move to a blank page tied to the index card and write away. No matter how much I jump around, I have my scenes identified with index cards when I click to the cork board. It's great to identify plot holes, to know where I need to develop a new scene. Can't do that with Word.
Short story, it's affordable, offers more than I've even began to tap into, and can keep you organized. Check it out.