If you are on a Mac (With all those Apple things, I assume so!), you might want to take a look at the application Papers.
I use it a lot, and even though it has been created for scientific journals, it should work just fine for you, as it is essentially a database for PDF's. You can see it as iTunes for PDF's, with collections, metadata, and so on..

It even has a iPod/iPhone/iPad application, which can sync with the Mac application, so again like iTunes..