I've started using Calibre for these purposes, saving papers from arXiv to it, and can definitely recommend. It takes a bit of manual effort to add tags to the papers, but once you have a bit of a collection going they autocomplete. The only downside is lack of read/reading/unread status, but I've hacked around it by rating papers and books I'm currently reading one star. I'd love to have an easier method for importing the papers, but not enough to actually have tried to write the script yet.