AllMyNotes Organizer is an outliner application for Windows, and it allows you to store all documents and notes in a single storage file.

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

DEVONthink a document and knowledge management app for the Mac.

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

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

myBase is a unique free-form database software that allows entry of unstructured text, webpages, images, documents, emails and even arbitrary files.

BeeCanvas is an online whiteboard based visual collaboration tool.

CintaNotes is a freemium Microsoft Windows notetaking program.

Elephant is a notetaker with a classic interface.

footnote is a very light and neat Notebook App for elementary OS.

Leanote is a self-hosted note taking app.

NixNote is an open source client for Evernote.