Are my thoughts better captured in words or in images? No problem, with pen and paper I can switch modes seamlessly, and, furthermore, mix them without any hassle. Should I come up with tags and some appropriate naming convention so I can find my notes later? No need—when everything is stowed away in a compact notebook, I can quickly flip through and find a multitude of phrases or doodles that indicate what subject I've explored. There's something charming, too, about flipping through the musky contents of a forgotten notebook that I find lacking when I peruse old digital files.
Plenty of people find digital solutions more appropriate, and sure, they do eliminate some of the hassle of carrying around a notebook and pen, they make notes easier to share with collaborators (this is where they excel!), and if you have a large number of notes it may serve for better organization, but at the end of the day, note-taking is one domain in which I've found newer tools aren't necessarily better tools. Something about the tactile and fluid experience of taking pen and paper notes still gets my neurons firing in the right ways...I think the persistence of whiteboards in the workplace also attests to the value of analog means for capturing our thoughts.