The other day I saw someone mention
Mendeley as a tool for tracking and
annotating papers (along with BibTeX entries). I've been impressed so
far. It can import PDFs and, as long as their metadata is reasonably
correct, it can usually figure everything out for you. If it fails,
you can just feed it the DOI for the paper and it looks up all of the
metadata for you.
It has fancy "cloud" and "social" features, but I think I can forgive
that. Time will tell.