Readwise - Effortlessly rediscover and organize your Kindle highlights
Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.
Knotes - An efficient, beautiful Kindle highlights & notes manager
Standard Notes - A safe place for your notes, thoughts, and life's work
Clippings.io - Organize the notes you make on your Kindle
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.