CherryTree - A hierarchical note taking application, featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.
Todoist - Todoist is a to-do list that helps you get organized, at work and in life.
Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.
Org mode - Org: an Emacs Mode for Notes, Planning, and Authoring
Zim Wiki - Zim is a graphical text editor used to maintain a collection of wiki pages. Each page can contain links to other pages, simple formatting and images.
Todo.txt - Track your tasks and projects in a plain text file, todo.txt. A todo.