For PDF's I recently discovered Mendeley. It's cross platform (currently using it on Windows and Ubuntu), and also offers a few gigabytes of free online storage for syncing books, if you want that feature. It has tagging and folder functionalities, tabbed interface, annotation tools, and remembers where you last left reading. Personally, I don't like the interface of Calibre and the fact that I found it to be quite slow.
However, it doesn't support ebook formats (e.g. epub), which is a shame since it is a really good free software. I recommend you still have a look at it though, like I did when I needed something to read books on and wasn't disappointed!