Book and citation managers for OS X
You should definitely look at Papers. The new version (Papers 2) was released a few weeks ago, and while not completely rock stable, I really can't live without it !

It has pretty much all the features you asked. You can manage books (and ebooks), each entry in the "database" is linked to one or more files (.pdf most of the time).

In addition in Papers 2 the citation process has been completely updated, you should have a look at their website about that.

There also a version for iOS and synchronization between your devices is apparently very easy.