Knotes - An efficient, beautiful Kindle highlights & notes manager
Readwise - Effortlessly rediscover and organize your Kindle highlights
Klib - Kindle & iBooks Highlights Manager
Pocket to Kindle (P2K) - Send articles saved in Pocket to your Kindle
Clippings.io - Organize the notes you make on your Kindle
Wellput - Export your Kindle highlights into a personalized library