For me it's to do with spatial organisation. If I'm working on something I normally have a large sheet of paper with all my tiny notes, and I know once I've written something down where it is - so I know that I scribbled down the background color over here, and the dimensions for that div over there...
The lack of any rigidity or standard form for input is also liberating. I can scribble down copy, lists, diagrams, flow charts, all with a single intuitive interface. Name an app that can claim that!
That's one thing I do miss, although using a bigger piece of paper makes the need to rearrange less frequent. I generally make notes like this only for transitory stuff, if I am sticking with paper notes for a big system then different bits will be on different pieces of paper, which allows easy rearranging.
The lack of any rigidity or standard form for input is also liberating. I can scribble down copy, lists, diagrams, flow charts, all with a single intuitive interface. Name an app that can claim that!