When I read a book I take notes on paper, because it's faster. I use these notes to summarize / reword the information for myself and to write down further references I should check up later. I usually try to copy the summaries manually into OneNote later. This helps me remember them better and saves them for further use.

For all other types of notes (thinking by writing - which I do a lot, random notes, web clips, contacts, to do lists, etc.) I use OneNote. I've been a heavy OneNote user for years, so my system is pretty robust and has tons of information in it, but it's all very simple to access with a click or two, and it's extremely organized.

I have a few OneNote notebooks that I put a privacy lock on, but I'd let my wife read them (she monitors my computer use anyway, so she can read them when she views what I typed).