I have myself tried:
* Calibre -> not the most beautiful UI/UX. Does it even sync across devices?
* Mendely -> Good for paper management.
* PapersApp -> Much better for paper management and research stuff.
* Kindle Cloud -> Only for epubs. I have epubs, pdfs, djvu.
* PDF viewer -> Files here and there and often in multiple places. Hard to manage across topics/genres.
* Preview (Apple) -> I can highlight. But files scattered.
* iBooks -> can't open PDF.
Personal frustration:
I'm cursed to live in permanent temporariness so far, but luckily am fully adept at spending countless hours reading books (and papers) on any screen. I read on various topics and usually just because I love consuming knowledge, and not necessarily hoping that I'd churn out a paper (so I don't care about bibliography/citation features). I guesstimated and realized I've read some 200 non-fiction books and around 70 papers in the last four year and I alway end up discovering some gems left in some folder. Now it bothers me so much that I'm planning to write a webapp just to solve this problem.