There is no 'modern' note taking app remotely as capable as Org-Mode. That said, there's a tradeoff to be made as to use Org-Mode effectively is a project in it

There is no 'modern' note taking app remotely as capable as Org-Mode. That said, there's a tradeoff to be made as to use Org-Mode effectively is a project in itself (check out a couple of youtube videos on it). In my experience it's also hard to use it without being thoroughly infected by emacs/lisp envy. Whether this is a good or bad thing is a metaphysical question.