Mendeley is good for this, and specifically designed for managing a library of academic papers. It supports tagging and full text searches, as well as some half-baked "social" features which can be safely ignored. The most useful feature for me is that it can watch a directory for new papers, and add them to its library as well as my directory tree (author/year/paper). It can also maintain a bibtex file for the entire library which is handy for citations.