Bookmark Tree - Web annotations VS RunaBook

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

Monkkee - Keep a private journal securely on the Internet – to provide a convenient user experience your...

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.

Idea Notebook - Idea Notebook is an app that allows you to keep track of your logs business ideas and track as well as organize them.

Diigo - Diigo is a powerful research tool and a knowledge-sharing community

Scrapbox - A new style of note-taking that lets you create, discuss, and learn together in one self-organizing space.