If you revel in scanning your documents and keeping an e-trace of all your correspondence, Yep is the PDF document management system for you. Yep organizes PDF files and allows you to tag them automatically based on the contents of the documents or define your own tags.
For academic papers, it can download tags and information from Google Scholar as well. The robust search engine allows you to search based on both Tags and contents (where legible). Give it a whirl. I have given Yep total control over my document organization.