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Makagiga is an open-source, easy-to-use, portable application for doing a variety of tasks, such as todo listing, text editing, or RSS reading. Plugins are used to implement its various capabilities.
UPDATE 2024: Get a new version here: https://github.com/ivoras/EncryptedNotepad2
"Encrypted Notepad" does only one thing, but aims to do it perfectly - a Notepad-like simple text editor where files are saved (and later loaded) encrypted with industrial strength algorithms. Available both for the desktop (as a Java application) and on Android.
Unencrypted data is never stored on-disk. Source is released (on SourceForge) under the BSD license.
Jarnal is a plattform-indepenent programm written in Java for notetaking, sketching and PDF-/picture-annotating. It works like a normal notepad with the difference of being digital. It is thought to be used with a stylus on tablet-pcs.
Tinboy is a notetaking application that combines ease of use and simplicity with sophisticated means to organize information.
It will be available as an Eclipse Plugin and notes can be shared using a revision control system like CVS.