I've always made notes in the margins of my books. When ebooks arrived on the scene, I searched for years to find the best way to sync my notes and highlights between books.
I finally found a solution a few months ago. I'm kinda embarrased to share this as it was right there all along. So you may laugh, but perhaps this post might help someone else.
First to be clear, the Amazon kindle app does a good job syncing notes and highlights, but what it neglects is books not purchased from amazon, like the pdf file I open in the kindle.
I tried several different pdf readers. Many offer great highlighting and commenting. But syncing these between my laptop, iPad and iMac was a problem.
I tried making edits on a pdf in dropbox, but the experience was never ideal. Each save required a sync time and often my highlights were not editable after I saved the pdf.
Then one day experimenting with iBooks I figured it out!! Now, this solution will only work if you've made a faustian deal with Apple. But I do love their stuff and was happy to do so.
When you buy an ebook, make sure you get a epub version. Then open this epub version from dropbox using ibooks from each device you wish to use.
You must initially open the epub document in ibooks from each device. When you do, you'll discover all your notes, highlight and even page location has been synced!
This may seem small, but when I finally figured this out, I wanted to shout from the mountain top!
Hopefully this helps someone else out there.