calibre - Ebook manager, viewer & converter
Readwise - Effortlessly rediscover and organize your Kindle highlights
FBReader - FBReader is an e-book reader for various platforms. Features:
Knotes - An efficient, beautiful Kindle highlights & notes manager
Google Play Books - Google Play Books lets you search, preview, and buy millions of books using Google Book Search.
Clippings.io - Organize the notes you make on your Kindle