Please write a single answer per comment to clearly see the most popular tools. Vote on the ones you like.
There were too many options in this post and I want to see what are the really interesting ones.
To complement this post:
What file-sharing and media organizing software do you wish that existed?
Calibre for organizing, converting, and syncing eBooks.
Absolutely vital for anyone who uses an ebooks.
I personally dislike it. It has a poor appearance and instead of copies books instead of tracking them wherever I want them to be. However, it is currently the best option available.