Used Evernote for a while, not even paid, but it doesn't offer anything (for me personally) that a flat folder with text or markdown files wouldn't cover. Then looking at the downside, I don't own the data and if Evernote decides they've had enough, all my stuff could be lost.

Tried doing plain files again (via Notable because people said so, but that also doesn't really offer anything an editor with markdown support (cmd + click to open other file) doesn't offer itself), but by then I didn't really need to keep notes anymore (I passed beyond the "research" phase of my current project).