Readwise - Effortlessly rediscover and organize your Kindle highlights
CryptoTE - CryptoTE is a text editor with integrated strong cryptography.
Klib - Kindle & iBooks Highlights Manager
Notebook PEA - Protects your private notes with a password.
Clippings.io - Organize the notes you make on your Kindle
Paranoia Text Encryption - Paranoia Text Encryption encrypts text according to a choice of strong algorithms.