If you use a Surface, or other modern, non-caveman computer with excellent pen support, then there is nothing better than OneNote for note-taking. Interestingly, MS has been slowly deprecating the legacy desktop version of OneNote in Office and replacing it with the free Windows 10 app, which is now far more capable than the old version was.
Of course, there still things that should be added - especially in the drawing, touch/pen UI (bring back radial menus!), and data management/tagging searching departments, but if you haven't tried it lately, OneNote has gotten staggeringly better over the past couple of years, and IMO, easily outstrips its current competition...