I'd highly recommend Chikoo- not only can you tag and organise your books but also access them directly- whether in pdf, zip, rar or Kindle. (Also does other files as you may have guessed, but its outstanding for books- you could also catalogue links to online articles and journals &c.)
I've also found great joy by setting text books (as from Project Gutenberg) to open with Tofu and accessing them from Chikoo- makes for a much more pleasant experience.