Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
Workflowy - A better way to organize your mind.
OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.
Indigrid - Plain text outliner with side-by-side views.
CherryTree - A hierarchical note taking application, featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.