GNU Emacs - GNU Emacs is an extensible, customizable text editor—and more.
Org mode - Org: an Emacs Mode for Notes, Planning, and Authoring
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
Orgzly - Outliner for notes, tasks and to-dos
Workflowy - A better way to organize your mind.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.