For GUI, NoteCase is my favorite. It's fast, lightweight and full of functionality (now it can even do some wiki-like things).
It's in the pinned "New Package Announcement" thread. There you'll also find a number of alternatives.
For CLI, I am studying Emacs Planner Mode. The great thing is there is no issue of syncing or cross flatform file sharing. Everything is done in plain text. And being able to implement GTD is the gem.