One app I love is Index Card. It is only available for iPad. It has been incredibly helpful in structuring my book. I can create cards, move them around, and even group cards. It provides a nice visual layout, and creates an outline from the card layout.
After writing about 10,000 words on the iPad, and introducing new characters and scenes, I decided it was time to find a writing app for my laptop. The only writing program I had was Pages, and I didn't feel like it was the right program for writing a novel.
I had heard great things about Scrivener, but was a little intimated by the vast amount of features. After trying a few demos of other products, I decided to give Scrivener a try. It is great! I'm still a little overwhelmed by the features, but I will learn them as I go, or as I need them. One great feature is that it syncs with Index Card on the iPad.
I still write on the iPad, but not as often as on the laptop. Most of my writing on the iPad is when it's a little more convenient (like laying in bed), and I usually only write quick highlights of a scene and some dialog. I use Dropbox to access the files from my iPad, and then polish them up in Scrivener on the laptop.
What tools do you use?