In regards to highlights and notes, I haven’t used clipping.io to capture my thoughts. Never heard of it, sadly. Instead I used to copy the highlights associated with each book to a Doc. Now with the update that Mariana mentioned you can add them to your Diigo collection. Only done this with one book so far. I like the idea of it, just frustrated that it is not a service that is more open. I guess Clipping.io was that service and they have closed it. What I like about highlights and digital texts in general is the ability to go back and search. I agree that paper maybe better for memory, but I find the ability to easily trawl texts priceless.
Like Alan, I feel like I regularly stumble upon forgotten services, worse is when you are still paying for them.