First off - I realize everyone's brains DO function differently - and Microsoft's OneNote isn't for everyone - BUT you should SERIOUSLY consider OneNote! I'm more of a mind-mapping kind of person, but the linear layout of OneNote has some real advantages. For example, I recently had a bit of a mind boggler. I was aggregating all the info from from of the products we sell and was quickly getting over my head (not hard, I know!). I had multiple categories of items and sub items and options to consider. My goal was to put all of this info into a format that I could easily browse through, both for my education and future reference. I ended up putting all the info into OneNote. It worked out beautifully! Each item and option had a full color PDF, so I was able to retain all that wonderful formatting and info in one place! 

I ended up with a problem. Almost all of my customer-facing and immediate reference materials are accessible to me through my iPad. I had no way to open the OneNote notebook on my iPad! A search through some Apps landed me at MobileNoter. MobileNoter allows me to sync my notebooks via the web or wifi! The formatting is very decent and I can even edit my notes with text, handwriting, photos and audio clips! 

Here's a quick video from their website!