I also find it useful to organize my notes by topic rather than by book/author/time. Over time, I will build a master reference for topics that I'm interested in.

OneNote/Evernote is especially helpful when you use handwritten idea maps (e.g. https://1drv.ms/u/s!AvGG5UqSCqXTnjq9_pD_gb7SJPce). I can't run out of space on my page and I can easily modify the contents if I find better material down the road.