I finally used the Scrivener software I bought with the 50% off discount I received after being a winner of Camp NaNoWriMo August 2012. The original price was something like $40, so that's not a bad price either.
I don't use physical index cards, but the index card feature on Scrivener is awesome! You can write your outline on them and move scenes around wherever you want just by clicking and dragging. The program puts the index cards together in an outline for you in another view. I'm still trying to figure out how to use the various tools, but I'll get to that as I go on.
The program saves your progress for you every 5 seconds or however long you set it to save. That way if you forget to save or the power goes out, your work is safe.
I plan on using Scrivener to write my future books from here on out.