Much as it shames me to admit it, I still prefer paper systems for just about everything other than very large or technical information collections. Anything involving art, the humanities, or social sciences and I'm definitely the notebook/wall chart/post-it
In my case it all comes down to who
the research is intended to be used by.
Since most of what I do is solely for my own
use, I don't feel a strong need to compile my sources for posterity or peer review . Something which seems to be the unvoiced motivation behind many 'reference' and 'organizer' type apps.
As long as I can easily find what I'm looking for when I need it, I prefer to keep things as simple as possible. Otherwise the method can take on a life of it's own and turn into an endless round of superfluous preparations to do research or "get organized" rather than actually doing it.
But maybe that's just me, selective closet Luddite that I am.