CherryTree is an hierarchical note taking application, featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.

FCorp My Calendar is a free software to manage a diary, notes, schedules, birthdays, etc.

Joplin is an open-source free note taking and to-do application.

nvALT 2 is a fork of the original Notational Velocity with some additional features and interface modifications, including MultiMarkdown functionality.

Guide is an application that allows you create documents ("guides") which inherently have a tree (which you can modify as you please) and text associated wit…

Evernote is a note taking application which keeps the notes taken in sync across all platforms using its cloud infrastructure.

Google Keep is a cloud based note taking application.

Notezilla is a sticky notes app for Windows.

ResophNotes is a fast note writing tool and a Simplenote client on Windows.

Tomboy is a desktop note-taking application for Linux, Unix, Windows, and Mac OS X.