I prefer org-mode[1] on emacs. It's simple, flexible, distraction free and for some reason reminds me of writing on paper. You get the simplicity, while also making it as powerful as you want.
Sometimes I'll capture to paper even if I'm sitting in front of my computer. If I've got something complex to reason through, I like the free-form nature of paper. I pretend it's an auxiliary scratch buffer whose contents I will reason about later.
My paper notebook, therefore becomes pretty nonsensical, because it isn't the system of record. I carry it as a notebook because I can always go back a day or two if I got lazy and didn't transcribe the previous day. Also a paper notebook puts on a better show for society as compared to just having a few sheets of printer paper along for the ride at meetings (though that works too). Periodically, I rip previous pages out (if spiral bound--they tear cleanly) and shred them just to restore that fresh notebook feeling.
I've seen people apparently use them to reasonable effect though, so I'm going to assume that people capable of note-taking on mobile are just a more evolved kind of human than I am :-)
In paper, I tend to really note-take. I like note-taking on paper for things I don't really understand yet. I prefer pre-writing in an app for situations where my understanding of the topic is good, and I want to skip steps (e.g. writing a blog post about a presentation, where the topic is already familiar)
Now, in fairness, I have recently started using SimpleMind for mind-mapping real-time. I find it does a good job at doing both things. It helps me build a narrative structure in one branch, while capturing notes in others. It also gives me a lot of nice flexibility on-screen to rearrange branches, relocate topics and do other general house-keeping.
It's response is sufficient to capture in paper like fashion.
I still prefer paper, but the little note app that ships with the phone works very well.
But usually I don't use my laptop during work. Instead I print just day's notes (schedule etc.) to a single paper sheet and keep the note paper with me. I do corrections and maybe add notes with a pen. Then later at home I modify my org-mode files to match my note paper.
I'm also surprised the article didn't mention mind mapping. Does nobody do that anymore?
In that way its benefits are similar to pen and paper.