Emacs + orgmode. Quite technical, not for the faint of heart, but it is an amazing tool to keep everything in plain text. If you are not a technical person, probably this is not for you, as it requires quite the tinkering, but once configured to your workflow, it is very good.

Second place for Manuskript (source code), that is an open source scrivener-like application. I like it a lot, but I always go back to emacs, but probably someone here can appreciate it.