Polar "makes it easy to manage your reading."
A powerful document manager for Mac, Windows, and Linux for managing web content, books, and notes - supports tagging, annotation, highlighting and keeps track of your reading progress.
Some caveats: I've only used Polar for a short time, and I have not yet tried all the features. For example, I haven't tried creating flashcards.
If you try it, feel free to share your experiences. Also, if you prefer a different tool, I'd be interested in hearing about it.