I came across gPapers this weekend, which is a relatively new application that bills itself as "iTunes for PDFs". It looks pretty good, with lots of features.
It uses pyGtk, so it's another scripted app, no compilation needed. It has separate lists for authors, organization, etc. as iTunes does for artists and albums. It does a pretty good job of searching online databases, and reading PDF files.
Being a new app, and having a few unusual library dependencies, you probably won't find it in your distribution's repository. So if you want to give gPapers a shot, you'll have to download and run it using the source.