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.