I write using Notepad++, which helps a lot with things like indenting and having a million tabs open at once (as I usually prefer). However, I do also take notes on paper, usually in rough flow-chart form, though they’ve been getting a lot less rough since Sabres of Infinity.
I’ve been trying to become more organised, taking more detailed notes and outlines, but it’s not a habit I can stick to very well, and I will very frequently improvise something when I realise that something that *should* be in the outline isn’t, or when something that is in the outline proves superfluous on second thought. Mecha Ace was far more thoroughly planned out than Sabres of Infinity was, and I think that let me get away with much more voluminous branches choice-wise (An average playthrough of SoI is about 1/3rd its total wordcount. For Mecha Ace, it’s more like 1/5th). Of course, that also means a lot more continuity errors, which is what CoG is helping me find and fix right now.