(1) I’m working on a book right now and am taking notes in Evernote, mainly because the OCR is convenient and the software lends itself to quick-and-dirty notes. I suspect that I need that kind of approach, because I tend to take notes that are super-neat, and I fear that they may become almost an end in themselves.
(2) I’m also working on another big project (a book eventually, I hope), and for that I’m using MyInfo, which has been my favorite note-taker for years. It’s beautiful on the screen (see my comment about neatness above), it has a nice UI, and it is easy to organize material. Its major shortcoming is that it is Windows only and hence not available on mobile devices.
(3) I’ve just begun using Documents by Readdle on my iPad. It’s an excellent file organizer and a solid reader of PDF (and other) documents. When I download a PDF of, for example, a book, I need to look through it carefully, marking it up as I go. Then I turn to Evernote or MyInfo for the actual note-taking.