Best app I have yet to use is hands down, Notability. It has the best organization and mimics much of OneNote. They also have amazing customer service and reply within a couple of hours.
They emailed me telling they are working on designing the ability to create subcategories inside the different subjects you have created. Once this happens, I will be thrilled and will have a OneNote replacement.
It also has a very easy method to export files as .PDFs to DropBox and other alike sharing services. This is now the only note taking app I use in class. I'd honestly be willing to pay $20 for this app, it definitely is underpriced and is a necessity for all students who use their iPad for notes.