Trello all day. Each book gets its own list. Each item in the list is something I want to remember.
Yes you have to write it out but this cost:
1. forces you to only save what matters 2. encourages you to compress the info which requires you to understand its essential parts
I record the notes as I encounter noteworthy things. At the end of a book the trello list is effectively a compressed book and index to the actual text.