I once wrote something about the tools I use on the Mac. As time goes by, however, this set of tools has changed, as has my work-flows.
I still use Evernote, but mainly for stuff that I want to save longterm. I use Pocket for the things that I just want to read later. It works nicely across computers and phone, so I often pocket something on one device and read it later on another (like on the phine on the train). Feedly is still in daily use, but I rarely open Flipboard.
The larger shift is in writing and research. Yes, still Markdown. Would never leave home without it - but I am slowly leaving Sublime Text in favor of Emacs.
Now, you could call me a masochist and a Luddite. Going for Emacs, now? Actually, the reason is orgmode, and I now believer that my earlier, botched attempts at making the siwtch was because I did not have any real reason and could not see the benefits. Deciding to use orgmode lead to Emacs, not the other way around.
I know that the whole one big text file-movement is already old hat and such, but it does still make sense. Firstly, plain text (with light markup such as Markdown) is eminently future and platform proof. One big file (or a couple of large files) as opposed to a larger number of small files is probably a matter of personal preference. I have used nvAlt a bit, and nvAlt is firmly in the many-small-files camp. But I got into orgmode and here fewer, larger files make so much more sense.
I would not necessarily recommend that you switch to Emacs. It can be painful and odd and frustrating. It is an experience from before cutesy UIs and from when users were supposed to be sentient beings. It is a window into the past. It is fun.